Stay tuned ...
BREAKING NEWS...
April 2019
Great news! Elisa Donati received the Best Poster Presenter Award at CECAM in Lausanne - QM/MM school, presenting her research work on enzyme catalysis -
Congrats to Elisa!!! https://www.cecam.org/school1716/
Great news! Elisa Donati received the Best Poster Presenter Award at CECAM in Lausanne - QM/MM school, presenting her research work on enzyme catalysis -
Congrats to Elisa!!! https://www.cecam.org/school1716/
April 2019
Into the rational design of gold-based nanoreceptors with targeted affinity and selectivity!
Another nice story from our great collaboration with the groups of Prof. F. Mancin and Prof. F. Rastrelli in the University of Padova.
"Molecular Dynamics Simulation-Directed Rational Design of Nanoreceptors with Targeted Affinity"
X. Sun, L. Riccardi, F. De Biasi, F. Rastrelli, M. De Vivo, and F. Mancin
Angewandte Chemie, 2019
Into the rational design of gold-based nanoreceptors with targeted affinity and selectivity!
Another nice story from our great collaboration with the groups of Prof. F. Mancin and Prof. F. Rastrelli in the University of Padova.
"Molecular Dynamics Simulation-Directed Rational Design of Nanoreceptors with Targeted Affinity"
X. Sun, L. Riccardi, F. De Biasi, F. Rastrelli, M. De Vivo, and F. Mancin
Angewandte Chemie, 2019
March 2019
Congratulations to Matteo Borella!
We prodly congratulate Matteo Borella, in our lab, who has just obtained his Master's degree on Chemical Engineering from the University of Genova, with the Cum Laude distinction!
He worked in our lab on coding and MD simulations of functionalized nanoparticles, in collaboration with Sebastian UF and Laura R.
Thesis title: Modeling and Simulations for the Engineering of Functionalized Nanoparticles.
Cheers!
Congratulations to Matteo Borella!
We prodly congratulate Matteo Borella, in our lab, who has just obtained his Master's degree on Chemical Engineering from the University of Genova, with the Cum Laude distinction!
He worked in our lab on coding and MD simulations of functionalized nanoparticles, in collaboration with Sebastian UF and Laura R.
Thesis title: Modeling and Simulations for the Engineering of Functionalized Nanoparticles.
Cheers!
March 2019
Mark your Calendar!
Marco De Vivo is part of the organizing committee in a handful of events of interest for the drug discovery community.
-SBDD 2019: "Structure-Based Drug Design (Computational Advances in Drug Discovery)" (September 23, 2019 - September 26, 2019). Sestri Levante, Italy. For more information, check out this link.
-CECAM Workshop: "Progress and developments of artificial intelligence for drug design" (June 17, 2019 - June 19, 2019). Genoa, Italy. For more information, check out this link.
-CECAM Workshop: "Challenges in modelling and simulations of nanoparticles in complex environments" (May 29, 2019 - May 31, 2019). Genoa, Italy. For more information, check out this link.
Mark your Calendar!
Marco De Vivo is part of the organizing committee in a handful of events of interest for the drug discovery community.
-SBDD 2019: "Structure-Based Drug Design (Computational Advances in Drug Discovery)" (September 23, 2019 - September 26, 2019). Sestri Levante, Italy. For more information, check out this link.
-CECAM Workshop: "Progress and developments of artificial intelligence for drug design" (June 17, 2019 - June 19, 2019). Genoa, Italy. For more information, check out this link.
-CECAM Workshop: "Challenges in modelling and simulations of nanoparticles in complex environments" (May 29, 2019 - May 31, 2019). Genoa, Italy. For more information, check out this link.
March 2019
The interview of Marco De Vivo for La Repubblica is now online! Check it out here.
Marco De Vivo talks to La Repubblica about the importance of the periodic table on the 150th anniversary of its design.
"E' l'alfabeto che ci permette di parlare con il mondo intorno a noi e che in futuro ci permetterà di costruire farmaci, materiali e metalli nuovi" ("It's the alphabet that allows us to talk with the world around us and that will allow us to come up with new drugs, materials, and metals in the future") - Marco De Vivo on the relevance of the periodic table.
The interview of Marco De Vivo for La Repubblica is now online! Check it out here.
Marco De Vivo talks to La Repubblica about the importance of the periodic table on the 150th anniversary of its design.
"E' l'alfabeto che ci permette di parlare con il mondo intorno a noi e che in futuro ci permetterà di costruire farmaci, materiali e metalli nuovi" ("It's the alphabet that allows us to talk with the world around us and that will allow us to come up with new drugs, materials, and metals in the future") - Marco De Vivo on the relevance of the periodic table.
March 2019
On the cover of JCTC! Check it out here.
"NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles"
S. Franco-Ulloa, L. Riccardi, F. Rimembrana, M. Pini, M. De Vivo
J. Chem. Theory Comput., 2019, 15 (3), 2022-2032.
Cover image created by Sebastian Franco-Ulloa
February 2019
NanoModeler is alive!
NanoModeler, your trusty webserver for the 3D modeling and parametrization of gold nanoparticles (AuNPs), is up and running.
Check out the webserver here.
And do not forget to take a look at its associated article here.
"NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles"
S. Franco-Ulloa, L. Riccardi, F. Rimembrana, M. Pini, M. De Vivo*
J. Chem. Theory Comput., 2019
NanoModeler is alive!
NanoModeler, your trusty webserver for the 3D modeling and parametrization of gold nanoparticles (AuNPs), is up and running.
Check out the webserver here.
And do not forget to take a look at its associated article here.
"NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles"
S. Franco-Ulloa, L. Riccardi, F. Rimembrana, M. Pini, M. De Vivo*
J. Chem. Theory Comput., 2019
December 2018
Christmas Dinner 2018
Marry Christmas and our best whises for a brilliant 2019 !!!
Christmas Dinner 2018
Marry Christmas and our best whises for a brilliant 2019 !!!
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Dinner with the group to celebrate the hard work and results of this year, looking forward to new challenges and findings, next year!
So proud of this group! Happy Holidays from us! 🎅🎅🎅❄️ Molecular Modeling and Drug Discovery Lab @ Istituto Italiano di Tecnologia |
November 2018
Marco De Vivo will present at the Structure-Based Drug Design 2018 meeting in Bali, Indonesia. Link
Marco De Vivo will present at the Structure-Based Drug Design 2018 meeting in Bali, Indonesia. Link
November 2018
NanoModeler is LIVE !!!
NanoModeler, our webserver for the building and parametriation of gold nanoparticles and nanoclusters, is ready to be used!
Take a look at the server, as well the manual and tutorials, at NanoModeler.it.
NanoModeler is LIVE !!!
NanoModeler, our webserver for the building and parametriation of gold nanoparticles and nanoclusters, is ready to be used!
Take a look at the server, as well the manual and tutorials, at NanoModeler.it.
November 2018
A new interview of Marco De Vivo for Rai Scuola is now online!
Marco De Vivo talks to Rai Scuola about the importance of computational biochemists in drug discovery.
Take a look at it on this link.
A new interview of Marco De Vivo for Rai Scuola is now online!
Marco De Vivo talks to Rai Scuola about the importance of computational biochemists in drug discovery.
Take a look at it on this link.
October 2018
MDV visited the President of Italy Mattarella at Quirinale, together with colleagues from IIT.
A great honor to meet the President, and be part of this event in support of the research against cancer in Italy.
Thanks AIRC and Thanks to our President!
MDV visited the President of Italy Mattarella at Quirinale, together with colleagues from IIT.
A great honor to meet the President, and be part of this event in support of the research against cancer in Italy.
Thanks AIRC and Thanks to our President!
From the Left: Davide De Pietri Tonelli, Valerio Voliani and MDV, from IIT
October 2018
Towards the mechanistic understanding of DNA and RNA polymerases!
In our latest perspective we discuss the state of the art, opportunities, and challenges that DNA and RNA polymerases bring along.
"The Catalytic Mechanism of DNA and RNA Polymerases"
V. Genna, E. Donati, M. De Vivo*
ACS Catal., 2018
Towards the mechanistic understanding of DNA and RNA polymerases!
In our latest perspective we discuss the state of the art, opportunities, and challenges that DNA and RNA polymerases bring along.
"The Catalytic Mechanism of DNA and RNA Polymerases"
V. Genna, E. Donati, M. De Vivo*
ACS Catal., 2018
October 2018
The interview of Marco De Vivo for Rai Scuola is now online!
Marco De Vivo talks to Rai Scuola about drug design from a computational perspective.
Take a look at it on this link.
The interview of Marco De Vivo for Rai Scuola is now online!
Marco De Vivo talks to Rai Scuola about drug design from a computational perspective.
Take a look at it on this link.
October 2018
Unraveling the allosteric communication in Protein Tyrosine Phosphatases!
Another recent publication from our great collaboration with the group of Prof. Jerome M. Fox in the University of Boulder, Colorado.
"Evolutionary Conserved Allosteric Communication in Protein Tyrosine Phosphatases"
M. Hjortness, L. Riccardi, A. Hongdusit, P. Zwart, B. Sankaran, M. De Vivo, J. Fox
Biochemistry, 2018
Unraveling the allosteric communication in Protein Tyrosine Phosphatases!
Another recent publication from our great collaboration with the group of Prof. Jerome M. Fox in the University of Boulder, Colorado.
"Evolutionary Conserved Allosteric Communication in Protein Tyrosine Phosphatases"
M. Hjortness, L. Riccardi, A. Hongdusit, P. Zwart, B. Sankaran, M. De Vivo, J. Fox
Biochemistry, 2018
September 2018
Towards a cell-permeable Protein Tyrosine Phosphatase inhibitor!
A recent publication from our great collaboration with the group of Prof. Jerome M. Fox in the University of Boulder, Colorado.
"Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation"
M. Hjortness, L. Riccardi, A. Hongdusit, A. Ruppe, M. Zhao, E. Kim, P. Zwart, B. Sankaran, H. Arthanari, M. Sousa, M. De Vivo*, J. Fox
Biochemistry, 2018
Towards a cell-permeable Protein Tyrosine Phosphatase inhibitor!
A recent publication from our great collaboration with the group of Prof. Jerome M. Fox in the University of Boulder, Colorado.
"Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation"
M. Hjortness, L. Riccardi, A. Hongdusit, A. Ruppe, M. Zhao, E. Kim, P. Zwart, B. Sankaran, H. Arthanari, M. Sousa, M. De Vivo*, J. Fox
Biochemistry, 2018
September 2018
Marco De Vivo presenting at "The Future of Enzyme Modelling"
Marco De Vivo will be delivering a talk on the understanding of enzymatic processing of DNA and RNA with computational approached. The conference will be held in Stockholm, Sweden on September 28 - 29, 2018.
Marco De Vivo presenting at "The Future of Enzyme Modelling"
Marco De Vivo will be delivering a talk on the understanding of enzymatic processing of DNA and RNA with computational approached. The conference will be held in Stockholm, Sweden on September 28 - 29, 2018.
September 2018
Marco De Vivo presenting at EuroQSAR 2018, Thessaloniki.
Marco De Vivo will be delivering a talk at the EuroQSAR2018 held in Thessaloniki, Greece. Four other members from our group will be joining with a poster presentation.
Marco De Vivo presenting at EuroQSAR 2018, Thessaloniki.
Marco De Vivo will be delivering a talk at the EuroQSAR2018 held in Thessaloniki, Greece. Four other members from our group will be joining with a poster presentation.
August 2018
Walter Rocchia and Pocketron
Pocketron, a new algorithm that examines pocket formation, dynamics and allosteric communication, was awarded as Emerging Technology at the 256th ACS National Meeting and Exposition, Boston.
"Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis "
J. La Sala, S. Decherchi, M. De Vivo, W. Rocchia
ACS Cent. Sci., 2017
Walter Rocchia and Pocketron
Pocketron, a new algorithm that examines pocket formation, dynamics and allosteric communication, was awarded as Emerging Technology at the 256th ACS National Meeting and Exposition, Boston.
"Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis "
J. La Sala, S. Decherchi, M. De Vivo, W. Rocchia
ACS Cent. Sci., 2017
August 2018
Marco De Vivo presenting at the ACS
Marco De Vivo delivered a talk at the 256th ACS National Meeting and Exposition, Boston. The talk described the use of molecular dynamics in the rationale design of intelligent nanoreceptors (a collaboration with Prof. Fabrizio Mancin).
Marco De Vivo presenting at the ACS
Marco De Vivo delivered a talk at the 256th ACS National Meeting and Exposition, Boston. The talk described the use of molecular dynamics in the rationale design of intelligent nanoreceptors (a collaboration with Prof. Fabrizio Mancin).
July 2018
Blocking topoisomerase to combat Cancer!
Another nice story from our great collaboration with the group of Dr. Osheroff at Vanderbilt University.
"Polyamine-containing etoposide derivatives as poisons of human type II topoisomerases: Differential effects on topoisomerase IIa and IIb"
A. A Oviatt, J. A Kuriappan, E. Minniti, K. R. Vann, P. Onuorah, A. Minarini, M. De Vivo, N. Osheroff
Bioorg. Med. Chem. Lett., 2018
Blocking topoisomerase to combat Cancer!
Another nice story from our great collaboration with the group of Dr. Osheroff at Vanderbilt University.
"Polyamine-containing etoposide derivatives as poisons of human type II topoisomerases: Differential effects on topoisomerase IIa and IIb"
A. A Oviatt, J. A Kuriappan, E. Minniti, K. R. Vann, P. Onuorah, A. Minarini, M. De Vivo, N. Osheroff
Bioorg. Med. Chem. Lett., 2018
July 2018
Our CECAM workshop entitled "Frontiers and challenges of computing metals for biochemical, medical and technological applications" was a lot of fun!
Thank you to all the speakers and participants !!!
Our CECAM workshop entitled "Frontiers and challenges of computing metals for biochemical, medical and technological applications" was a lot of fun!
Thank you to all the speakers and participants !!!
July 2018
On the cover of Nature Reviews Chemistry !!!
"Metal-ligand interactions in drug design"
L. Riccardi, V. Genna, M. De Vivo
Nature Reviews Chemistry., 2018, 2, 100-112.
Cover image created by Laura Riccardi (First Author).
June 2018
Our Perspective in Nature Reviews Chemistry !
Metal -ligand interactions in drug design. (Link)
Our Perspective in Nature Reviews Chemistry !
Metal -ligand interactions in drug design. (Link)
May 2018
Elirosa Minniti succesfully defended her PhD work on the design, synthesis, and characterization of anticancer compounds. Congratulations Elirosa!
Elirosa Minniti succesfully defended her PhD work on the design, synthesis, and characterization of anticancer compounds. Congratulations Elirosa!
May 2018
We welcome Andrés Felipe Vásquez Jiménez, who will be staying with us for a few months, visiting from the Universidad de los Andes - Bogotà, Colombia, where he works under the supervision of Prof. Andrés González.
We welcome Andrés Felipe Vásquez Jiménez, who will be staying with us for a few months, visiting from the Universidad de los Andes - Bogotà, Colombia, where he works under the supervision of Prof. Andrés González.
April 2018
Our project NANOMOTION has been funded with 36 millions of core hours of computer time by the European #PRACE for High-Performance Computing.
"MD simulations of nanoparticles with programmed recognition abilities"
In collaboration with the experimental group of Prof. F. Mancin at the University of Padua.
Thanks to PRACE, to Laura Riccardi in my group, and to all other collaborators !!!
Exciting times ahead!!!
Our project NANOMOTION has been funded with 36 millions of core hours of computer time by the European #PRACE for High-Performance Computing.
"MD simulations of nanoparticles with programmed recognition abilities"
In collaboration with the experimental group of Prof. F. Mancin at the University of Padua.
Thanks to PRACE, to Laura Riccardi in my group, and to all other collaborators !!!
Exciting times ahead!!!
April 2018
"L’importanza di comunicare i risultati della ricerca senza sensazionalismi",
by De Vivo Marco on @primocanale, CLIK HERE: https://bit.ly/2JlbDNM
"L’importanza di comunicare i risultati della ricerca senza sensazionalismi",
by De Vivo Marco on @primocanale, CLIK HERE: https://bit.ly/2JlbDNM
March 2018
A Video Interview to Marco De Vivo, for Il Corriere Della Sera - CORRIERE TV Salute.
Marco was interviewed by Luigi Ripamonti, on "how to make therapeutic drugs, today":
CLICK HERE: Link
A Video Interview to Marco De Vivo, for Il Corriere Della Sera - CORRIERE TV Salute.
Marco was interviewed by Luigi Ripamonti, on "how to make therapeutic drugs, today":
CLICK HERE: Link
Feb 2018
A new paper published in JACS, on how polymerases shape the growing DNA !
Watson-Crick model: to be or not to be...
read more here: (Link)
Congratulations to Vito Genna for this new study and result!
A new paper published in JACS, on how polymerases shape the growing DNA !
Watson-Crick model: to be or not to be...
read more here: (Link)
Congratulations to Vito Genna for this new study and result!
On the cover of JACS
March 7, 2018, Volume 140, Issue 9
"A strategically located Arg/Lys residue promotes correct base paring during nucleic acid biosynthesis in polymerases"
V. Genna, P. Carloni, M. De Vivo
J. Am. Chem. Soc., 2018, 140 (9), pp 3312–3321
Cover image created by Vito Genna
March 7, 2018, Volume 140, Issue 9
"A strategically located Arg/Lys residue promotes correct base paring during nucleic acid biosynthesis in polymerases"
V. Genna, P. Carloni, M. De Vivo
J. Am. Chem. Soc., 2018, 140 (9), pp 3312–3321
Cover image created by Vito Genna
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Feb 2018
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Our work on the cover of the Journal of Medicinal Chemistry !
New human topoisomerase II inhibitors to fight cancer. J. A. Ortega, L. Riccardi, et al. "Pharmacophore hybridization to discover novel Topoisomerase II poisons with promising antiproliferative activity" J. Med. Chem. 2018 – (Link) Cover image created by Laura Riccardi - cheers! |
Feb 2018
We welcome Nicoletta Brindani, who joins our group as postdoc in medicinal chemistry.
Nicoletta graduated from the University of Parma, Italy. Welcome Nicoletta !
We also wish the best of luck to Jose (Tony) Ortega, who has become Research Scientist at IIT.
After 5 years as a postdoc with us, Tony is now Researcher in Dr. Cavalli's group in IIT. Congratulations Tony!
We welcome Nicoletta Brindani, who joins our group as postdoc in medicinal chemistry.
Nicoletta graduated from the University of Parma, Italy. Welcome Nicoletta !
We also wish the best of luck to Jose (Tony) Ortega, who has become Research Scientist at IIT.
After 5 years as a postdoc with us, Tony is now Researcher in Dr. Cavalli's group in IIT. Congratulations Tony!
Feb 2018
A new paper out on Bacterial Topoisomerase and Novel Bacterial Topoisomerase Inhibitors !
Just published as part of the Special Issue "DNA Topoisomerases" of International Journal of Molecular Sciences - (Link)
This study was in collaboration with Dr. Miscione at the University de los Andes, Colombia.
Congratulations to Sebastian Franco-Ulloa and Giuseppina La Sala, co-first authors !
A new paper out on Bacterial Topoisomerase and Novel Bacterial Topoisomerase Inhibitors !
Just published as part of the Special Issue "DNA Topoisomerases" of International Journal of Molecular Sciences - (Link)
This study was in collaboration with Dr. Miscione at the University de los Andes, Colombia.
Congratulations to Sebastian Franco-Ulloa and Giuseppina La Sala, co-first authors !
Jan 2018
We welcome Adam Pecina, who joins our group as postdoc in computational chemistry.
Adam Graduated and comes from the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (Prage, CZ). Welcome Adam!
Vito Genna leaves our group after 4 years to join as postdoc fellow the group of Prof. Orozco at the Institute of Biomedical Research - Barcelona. Good luck, Vito!
We welcome Adam Pecina, who joins our group as postdoc in computational chemistry.
Adam Graduated and comes from the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (Prage, CZ). Welcome Adam!
Vito Genna leaves our group after 4 years to join as postdoc fellow the group of Prof. Orozco at the Institute of Biomedical Research - Barcelona. Good luck, Vito!
Dec 2017
A new paper out on two-metal-ion enzymes dealing with DNA and RNA !
Click here to know more.
Just published on Structure - Cell Press - click here: Link
This study is in collaboration with Marco Marcia's Lab at EMBL - Grenoble.
Congratulations to Vito Genna and to all the other co-authors!
A new paper out on two-metal-ion enzymes dealing with DNA and RNA !
Click here to know more.
Just published on Structure - Cell Press - click here: Link
This study is in collaboration with Marco Marcia's Lab at EMBL - Grenoble.
Congratulations to Vito Genna and to all the other co-authors!
Nov 2017
We welcome 2 new members of our groups!
Jissy Kuriappan, Postdoc funded by a Marie Skłodowska-Curie Individual Fellowship
Sebastian Franco Ulloa, who will start his PhD with us.
Looking forward to exciting projects, together!
We welcome 2 new members of our groups!
Jissy Kuriappan, Postdoc funded by a Marie Skłodowska-Curie Individual Fellowship
Sebastian Franco Ulloa, who will start his PhD with us.
Looking forward to exciting projects, together!
Oct 2017
A new paper out on targeting topoisomerase II:
Novel Topoisomerase II poisons with promising antiproliferative activity
Just published on J. Med Chem. - Link
Congratulations to Tony Ortega, Laura Riccardi, and all the other co-authors!
This paper is the result of a collaboration with Prof. Claudia Sissi (University of Padua) and Prof. Anna Minarini (University of Bologna).
A new paper out on targeting topoisomerase II:
Novel Topoisomerase II poisons with promising antiproliferative activity
Just published on J. Med Chem. - Link
Congratulations to Tony Ortega, Laura Riccardi, and all the other co-authors!
This paper is the result of a collaboration with Prof. Claudia Sissi (University of Padua) and Prof. Anna Minarini (University of Bologna).
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On the cover of WIREs Computational Molecular Science
M. De Vivo* and A. Cavalli “Recent advances in dynamic docking for drug discovery”, WIREs Computational Molecular Science, 2017 - (Link) Cover Article Cover image created by Giuseppina La Sala and Stefania La Sala |
Sept 2017
- My comments on Quantum Computing and drug discovery, in this article published in Science, "Quantum computer simulates largest molecule yet, sparking hope of future drug discoveries" - by Gabriel Popkin. Link
Sept 2017
On the cover of ACS Central Science
September 27, 2017
Volume 3, Issue 9
Pages 914-1055
G. La Sala, S. Decherchi, M. De Vivo*, W. Rocchia
“Allosteric communication networks in proteins revealed through pocket crosstalk analysis”,
ACS Central Science, 2017 – Just Accepted
• Highlighted in First Reactions ACS Central Science,
"Toward Understanding “the Ways” of Allosteric Drugs", by R. Amaro 2017
On the cover of ACS Central Science
September 27, 2017
Volume 3, Issue 9
Pages 914-1055
G. La Sala, S. Decherchi, M. De Vivo*, W. Rocchia
“Allosteric communication networks in proteins revealed through pocket crosstalk analysis”,
ACS Central Science, 2017 – Just Accepted
• Highlighted in First Reactions ACS Central Science,
"Toward Understanding “the Ways” of Allosteric Drugs", by R. Amaro 2017
July 2017
A NEW PAPER OUT IN CHEM !
Our paper on nanoparticle is on the cover of Chem - Cell Press!
This is a collaboration with the experimental group of Prof. F. Mancin and Prof. F. Rastrelli, at the University of Padova.
The first author is Laura Riccardi.
Check it out!
L. Riccardi, L. Gabrielli, X. Sun, F. De Biasi, F. Rastrelli, F. Mancin, M. De Vivo*
“Nanoparticle-based receptors mimic protein-ligand recognition”
Chem (from Cell Press), 2017, 3, 92–109
A NEW PAPER OUT IN CHEM !
Our paper on nanoparticle is on the cover of Chem - Cell Press!
This is a collaboration with the experimental group of Prof. F. Mancin and Prof. F. Rastrelli, at the University of Padova.
The first author is Laura Riccardi.
Check it out!
L. Riccardi, L. Gabrielli, X. Sun, F. De Biasi, F. Rastrelli, F. Mancin, M. De Vivo*
“Nanoparticle-based receptors mimic protein-ligand recognition”
Chem (from Cell Press), 2017, 3, 92–109
June 2017
Two new papers from our group!
1. Fighting melanoma!
Check out our new paper on J. Med. Chem. reporting the design and discovery of potent inhibitors of the enzyme Acid Ceramidase - Link
Congratulations to Tony Ortega, Pepe Arencibia, and all the other co-authors!
2. Dynamic docking - Our Opinions&Comments on "dynamic docking" for drug discovery in WIREs Computational Molecular Science. Read "Recent advances in dynamic docking for drug discovery" - Link
Two new papers from our group!
1. Fighting melanoma!
Check out our new paper on J. Med. Chem. reporting the design and discovery of potent inhibitors of the enzyme Acid Ceramidase - Link
Congratulations to Tony Ortega, Pepe Arencibia, and all the other co-authors!
2. Dynamic docking - Our Opinions&Comments on "dynamic docking" for drug discovery in WIREs Computational Molecular Science. Read "Recent advances in dynamic docking for drug discovery" - Link
June 2017
MarcoDV is presenting our combined experimental-computational work on nanoparticles at the 7th edition of the International Conference on Computational Methods for Coupled Problems in Science and Engineering (COUPLED PROBLEMS 2017), on 12 - 14 June 2017 on the island of Rhodes, in Greece.
This work is in collaboration with the experimental groups of F. Mancin and F. Rastrelli, at the university of Padova, Italy.
MarcoDV is presenting our combined experimental-computational work on nanoparticles at the 7th edition of the International Conference on Computational Methods for Coupled Problems in Science and Engineering (COUPLED PROBLEMS 2017), on 12 - 14 June 2017 on the island of Rhodes, in Greece.
This work is in collaboration with the experimental groups of F. Mancin and F. Rastrelli, at the university of Padova, Italy.
June 2017
VitoG will preset a poster on his doctoral work at the RNA and DNA Processes Throughout Biology: Mechanistic Insights and Applications to Human Health Gordon Research Conference at the University of New England Biddeford, ME.
VitoG will preset a poster on his doctoral work at the RNA and DNA Processes Throughout Biology: Mechanistic Insights and Applications to Human Health Gordon Research Conference at the University of New England Biddeford, ME.
May 2017
MarcoDV is visiting Vanderbilt University, for a seminar and collaborative effort on small molecules to fight cancer!
MarcoDV is visiting Vanderbilt University, for a seminar and collaborative effort on small molecules to fight cancer!
May 2017
Proud to be at the Self-Assembly & Supramolecular Chemistry Gordon Research Conference in Les Diablerets, Switzerland, where RiccardiL will present a poster on our recent work on molecular simulations for nanoparticles and chemosensing - This work is in collaboration with the experimental groups of F. Mancin and F. Rastrelli, at the university of Padova, Italy.
Proud to be at the Self-Assembly & Supramolecular Chemistry Gordon Research Conference in Les Diablerets, Switzerland, where RiccardiL will present a poster on our recent work on molecular simulations for nanoparticles and chemosensing - This work is in collaboration with the experimental groups of F. Mancin and F. Rastrelli, at the university of Padova, Italy.
April 2017
Two new PhDs from our group!!!
Congratulations to GiuseppinaLS and VitoG, who have successfully defended their PhD work!!!
Happy and proud for this!!! Best of luck for their career!
Two new PhDs from our group!!!
Congratulations to GiuseppinaLS and VitoG, who have successfully defended their PhD work!!!
Happy and proud for this!!! Best of luck for their career!
April 2017
MDV has presented at the 253rd American Chemical Society meeting in San Francisco, where he has also received the ACS OpenEye Outstanding Junior Faculty Award, Spring 2017 !
MDV has presented at the 253rd American Chemical Society meeting in San Francisco, where he has also received the ACS OpenEye Outstanding Junior Faculty Award, Spring 2017 !
March 2017
- My comments on Quantum computers, MD simulations, and drug discovery, in this article published on Chemistry World - by Katrina Kramer. Link
- MarcoDV is a speaker at the workshop organized by AIRC (Italian Association for Cancer Research), called "‘AIRC nelle scuole’, on March 9, in Genoa.
February 2017
Congratulations to Giuseppina LS ! She will be presenting "Molecular Simulations to Unravel the Allosteric Interplay between the SH2 Domain and A-loop Plasticity in Protein Kinases" at the 61st Annual Meeting of the Biophysical Society. February 11-15, 2017, New Orleans, Louisiana. These results are presented in our recent JCTC paper published here.
One more interview on our research activities has been published on "Il Resto Del Carlino", by Maddalena De Franchis.
Congratulations to Giuseppina LS ! She will be presenting "Molecular Simulations to Unravel the Allosteric Interplay between the SH2 Domain and A-loop Plasticity in Protein Kinases" at the 61st Annual Meeting of the Biophysical Society. February 11-15, 2017, New Orleans, Louisiana. These results are presented in our recent JCTC paper published here.
One more interview on our research activities has been published on "Il Resto Del Carlino", by Maddalena De Franchis.
February 2017
GREAT NEWS: We will be the host lab of a Marie Skłodowska-Curie Individual Fellowship !
GREAT NEWS: We will be the host lab of a Marie Skłodowska-Curie Individual Fellowship !
February 2017
An interview to MDV on our research activities has been published on the February issue of "Le Scienze", the italian edition of the "Scientific American".
A great privilege!
An interview to MDV on our research activities has been published on the February issue of "Le Scienze", the italian edition of the "Scientific American".
A great privilege!
January 2017
Our new paper just accepted on BBA - Molecular and Cell Biology of Lipids
This study proposes a mechanism regulated by lid domain plasticity and lipid flexibility for enzyme specificity in human monoacylglycerol lipase (MAGL) - a promising target for drug discovery.
Congratulations to LauraR, postdoc in our group, and all the other co-authors!
Our new paper just accepted on BBA - Molecular and Cell Biology of Lipids
This study proposes a mechanism regulated by lid domain plasticity and lipid flexibility for enzyme specificity in human monoacylglycerol lipase (MAGL) - a promising target for drug discovery.
Congratulations to LauraR, postdoc in our group, and all the other co-authors!
January 2017
Our project on molecular simulations for the study of enzymatic processing and selectivity of lipids in lipases has been funded by CINECA, through the ISCRA (Italian SuperComputing Resource Allocation) call. We received 500,000 hours on the new supercomputing machine MARCONI-A2.
This project is carried out by Laura Riccardi, in our group -
Excellent way to start a new year!
Our project on molecular simulations for the study of enzymatic processing and selectivity of lipids in lipases has been funded by CINECA, through the ISCRA (Italian SuperComputing Resource Allocation) call. We received 500,000 hours on the new supercomputing machine MARCONI-A2.
This project is carried out by Laura Riccardi, in our group -
Excellent way to start a new year!
December 2016
Christmas Dinner 2016
Marry Christmas and our best whises for a wonderful 2017 !!!
Christmas Dinner 2016
Marry Christmas and our best whises for a wonderful 2017 !!!
From the left: Roberto Gaspari, Marco DV, Laura Riccardi, Pepe Arencibia, Tony Ortega, Marco Borgogno, Vito Genna and Giuseppina La Sala
December 2016
MarcoDV has been awarder an Investigator Grant by the Italian Association for Cancer Research (Associazione Italiana per la Ricerca sul Cancro, AIRC), for the period 2017-2020.
We are grateful to AIRC for supporting our research !
MarcoDV has been awarder an Investigator Grant by the Italian Association for Cancer Research (Associazione Italiana per la Ricerca sul Cancro, AIRC), for the period 2017-2020.
We are grateful to AIRC for supporting our research !
November 2016
ACS OpenEye Outstanding Junior Faculty Award to Marco De Vivo !
MarcoDV has been selected for the ACS OpenEye Outstanding Junior Faculty Award for Spring 2017
Read more here: Link
Happy, proud and grateful for this Award !!!
This news has gained wide visibility in the Italian Media and social network, with articles and interviews.
Glad, proud and grateful for these opportunities to let people know about our work and results!
Click here: Link - Interview to MarcoDV on Oggiscienze
Click here: Link - news in english on researchitaly.it (the portal of Italian research)
ACS OpenEye Outstanding Junior Faculty Award to Marco De Vivo !
MarcoDV has been selected for the ACS OpenEye Outstanding Junior Faculty Award for Spring 2017
Read more here: Link
Happy, proud and grateful for this Award !!!
This news has gained wide visibility in the Italian Media and social network, with articles and interviews.
Glad, proud and grateful for these opportunities to let people know about our work and results!
Click here: Link - Interview to MarcoDV on Oggiscienze
Click here: Link - news in english on researchitaly.it (the portal of Italian research)
November 2016
OUTREACHING ACTIVITIES: Our research activities and last research articles are in the news - exciting!
Read here:
Link1 - Article in Corriere Romagna
Link2 - Article in RItalia online.
Link3 - Article in MIT Technology review
LInk4 - Article in TP24.it
Click here to download the article appeared on "il Secolo XIX" on the fundraising campaign to sustain AIRC (Italian Association for Cancer Research). This article also reports on some of our research funded by AIRC.
Great initiative!
OUTREACHING ACTIVITIES: Our research activities and last research articles are in the news - exciting!
Read here:
Link1 - Article in Corriere Romagna
Link2 - Article in RItalia online.
Link3 - Article in MIT Technology review
LInk4 - Article in TP24.it
Click here to download the article appeared on "il Secolo XIX" on the fundraising campaign to sustain AIRC (Italian Association for Cancer Research). This article also reports on some of our research funded by AIRC.
Great initiative!
November 2016
On the cover of JACS !!!
and also in JACS spotlights !!!
Our recent paper Genna et al., entitled "A self-activated mechanism for nucleic acid polymerization catalyzed by DNA/RNA polymerases" is on the cover of J. Am. Chem. Soc. ! (Link)
This paper is also highlighted in JACS spotlights - see here:
ACS Spotlights, "Polymerases May Progress with the Help of Hydrogen Bonding", by Deirdre Lockwood (Ph.D.)
J. Am. Chem. Soc., 2016, 138 (44), pp 14507–14508
On the cover of JACS !!!
and also in JACS spotlights !!!
Our recent paper Genna et al., entitled "A self-activated mechanism for nucleic acid polymerization catalyzed by DNA/RNA polymerases" is on the cover of J. Am. Chem. Soc. ! (Link)
This paper is also highlighted in JACS spotlights - see here:
ACS Spotlights, "Polymerases May Progress with the Help of Hydrogen Bonding", by Deirdre Lockwood (Ph.D.)
J. Am. Chem. Soc., 2016, 138 (44), pp 14507–14508
|
November 9, 2016
Volume 138, Issue 44 Pages 14507-14808 About the Cover: Ternary DNA/RNA polymerase (Pol) complexes show the formation of the previously unrecognized intramolecular H-bond formed by the nucleophilic 3′-OH and the β-phosphate of the incoming nucleotide. The illustration shows this crucial element used to propose and compute a novel self-activated mechanism (SAM) for nucleic acid polymerization in Pols. |
November 2016
On the cover of JCTC !!!
Our recent paper La Sala et al., entitled "HRD motif as the central hub of the signaling network for activation loop autophosphorylation in Abl kinase" is on the cover of the J. Chem. Theory Comput. ! (Link)
Congratulations to GiuseppinaLS and all the other co-authors!
On the cover of JCTC !!!
Our recent paper La Sala et al., entitled "HRD motif as the central hub of the signaling network for activation loop autophosphorylation in Abl kinase" is on the cover of the J. Chem. Theory Comput. ! (Link)
Congratulations to GiuseppinaLS and all the other co-authors!
|
November 8, 2016
Volume 12, Issue 11 Pages 5235-5680 About the Cover: On the left, the image shows the Abelson (Abl) tyrosine kinase and some distinct structural factors that form the signal transmission network for optimal function. On the right, the signal transmission network is artistically represented as several gear wheels. These suggest how distal structural motifs in proteins are interconnected and, here, how these must act synchronously so to modulate and favor the activation loop trans-autophosphorylation in Abl, as revealed by extensive MD and enhanced sampling simulations of multiple Abl systems. |
September 2016
- Our new paper out in J. Chem. Theory Comput. !
Our study reveals the signaling network for activation loop autophosphorylation in Abl kinase -
Congratulations to GiuseppinaLS and all the other co-authors!
check it out! - Link
- Our new paper out in J. Chem. Theory Comput. !
Our study reveals the signaling network for activation loop autophosphorylation in Abl kinase -
Congratulations to GiuseppinaLS and all the other co-authors!
check it out! - Link
September 2016
MarcoDV at the EMBL in Grenoble for a seminar and a visit to the synchrotron and powerful infrastructures for structural biology.
MarcoDV at the EMBL in Grenoble for a seminar and a visit to the synchrotron and powerful infrastructures for structural biology.
September 2016
LauraR, GiuseppinaLS and VitoG from our group will present Posters at the 21st EuroQSAR 2016 Conference, held in Verona (Link)
LauraR, GiuseppinaLS and VitoG from our group will present Posters at the 21st EuroQSAR 2016 Conference, held in Verona (Link)
August 2016
- One new paper out on a novel mechanism for RNA and DNA polymerase catalysis !
Check out our new paper on SAM, a novel and efficient Self-Activated Mechanism for DNA and RNA polymerases. This study is now published in the J. Am. Chem. Soc. - check it out! Link
Congratulations to VitoG and all the other co-authors!
- One new paper out on a novel mechanism for RNA and DNA polymerase catalysis !
Check out our new paper on SAM, a novel and efficient Self-Activated Mechanism for DNA and RNA polymerases. This study is now published in the J. Am. Chem. Soc. - check it out! Link
Congratulations to VitoG and all the other co-authors!
August 2016
MarcoDV will be delivering two talks at the 252nd ACS meeting in Philadelphia (21-25 August) - Meeting friends and colleagues, in Philly!
MarcoDV will be delivering two talks at the 252nd ACS meeting in Philadelphia (21-25 August) - Meeting friends and colleagues, in Philly!
July 2016
MDV invited speaker at the Gordon Research Conference on Comp Chem, held in Girona, Spain - July 24-29, 2016 Link
Vito, from our group, selected speaker at the Gordon Research Seminars, on 23-24 July. Link
Great events!!!
MDV invited speaker at the Gordon Research Conference on Comp Chem, held in Girona, Spain - July 24-29, 2016 Link
Vito, from our group, selected speaker at the Gordon Research Seminars, on 23-24 July. Link
Great events!!!
June 2016
Vito, from our group, will participate to the forthcoming EMBO workshop entitled "The biochemistry and chemistry of biocatalysis: From understanding to design". Vito will present a poster on our recent studies on human DNA Polymerase-η.
Vito, from our group, will participate to the forthcoming EMBO workshop entitled "The biochemistry and chemistry of biocatalysis: From understanding to design". Vito will present a poster on our recent studies on human DNA Polymerase-η.
May 2016
- Great CECAM meeting on Structural and Functional Annotation of Bioinorganic Systems at Scuola Normale Superiore in Pisa!
MDV among the invited speakers. Vito, from our group, will also present his work.
Check it out
- This month, MDV was also invited to deliver a lecture at the 'Universita' degli Studi di Milano', visiting Prof. Giorgio Colombo's group. Great visit!
- Great CECAM meeting on Structural and Functional Annotation of Bioinorganic Systems at Scuola Normale Superiore in Pisa!
MDV among the invited speakers. Vito, from our group, will also present his work.
Check it out
- This month, MDV was also invited to deliver a lecture at the 'Universita' degli Studi di Milano', visiting Prof. Giorgio Colombo's group. Great visit!
May 2016
- One new paper out in Biochemistry !
A computational investigation on catalysis of the Human Carnosinase Enzyme CN1 - an important target for drug discovery”
has been just published on Biochemistry (Link)
This is a paper in collaboration with the IAS-5 / INM-9 Computational Biomedicine Institute at the Forschungszentrum, Jülich
- One new paper out in Biochemistry !
A computational investigation on catalysis of the Human Carnosinase Enzyme CN1 - an important target for drug discovery”
has been just published on Biochemistry (Link)
This is a paper in collaboration with the IAS-5 / INM-9 Computational Biomedicine Institute at the Forschungszentrum, Jülich
April 2016
- On the cover of NAR !
Our new article Genna et al, entitled "Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η", is on the cover of the issue (April 7) of Nucleic Acids Res. ! (Link)
- On the cover of NAR !
Our new article Genna et al, entitled "Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η", is on the cover of the issue (April 7) of Nucleic Acids Res. ! (Link)
|
Legend:
DNA Polymerase-η (Pol-η) bypasses UV-induced DNA damages via a two-metal-ion mechanism that assures DNA strand elongation and correct genetic inheritance to the new cells generation. Two identical ternary complexes formed by Pol-η, double strand DNA and the incoming nucleotide, are shown. The coordination to the key two metal ions, in the active site, is displayed in the protein on the front. The complex in the back suggests a DNA-damage caused by UV light. |
February 2016
- One new paper out on DNA replication !
A new article from Vito Genna et al, entitled "Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η", has been just accepted on Nucleic Acids Res.
This study explains an effective and cooperative mechanism for DNA repair catalyzed by human DNA Polymerase-η.
- One new paper out on DNA replication !
A new article from Vito Genna et al, entitled "Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η", has been just accepted on Nucleic Acids Res.
This study explains an effective and cooperative mechanism for DNA repair catalyzed by human DNA Polymerase-η.
February 2016
- One new paper out !
A new perspective entitled "Role of Molecular Dynamics and Related Methods in Drug Discovery", is now on J. Med. Chem. - Link
This Perspective is part of the special issue "Computational Methods for Drug Discovery and Design"
This article is also F1000 Prime Recommended, click below!
- One new paper out !
A new perspective entitled "Role of Molecular Dynamics and Related Methods in Drug Discovery", is now on J. Med. Chem. - Link
This Perspective is part of the special issue "Computational Methods for Drug Discovery and Design"
This article is also F1000 Prime Recommended, click below!
January 2016
We welcome Sebastián Franco Ulloa, who will be staying with us for a few months, visiting from the Universidad de los Andes - Bogotà, Colombia, where he works in the computational group of Prof. Gian Pietro Miscione.
December 2015
Christmas dinner and picture!
Merry Christmas and a Happy New Year!
Christmas dinner and picture!
Merry Christmas and a Happy New Year!
From the left: Vito Genna, MarcoDV, Laura Riccardi, Pepe Arencibia, Tony Ortega, Marco Borgogno
November 2015
- One new paper out on Polypharmacology !
Our communication on ChemMedChem explains the molecular bases for dual inhibition of FAAH and COX enzymes - Check here
- One new paper out on Polypharmacology !
Our communication on ChemMedChem explains the molecular bases for dual inhibition of FAAH and COX enzymes - Check here
October 2015
- The John von Neumann Institute for Computing (NIC) granted 550,000 core-h on JURECA supercomputer at the Jülich Supercomputing Centre (JSC) to the group of Prof. Paolo Carloni, for a project in collaboration with Vito Genna and MarcoDV. The project is a continuation of an ongoing research effort focused on QM/MM simulations to decipher catalysis of enzymes involved in DNA repairing mechanisms.
- Marco Borgogno, after working in our Lab for ~one year on the design and synthesis of small molecules for anticancer drug discovery, today, Oct 27, has defended his undergraduate thesis, and graduated ... Summa Cum Laude!
An enthusiastic selfie :) ... with MarcoB, Tony (Ortega) and Alessandra.
October 2015
In the occasion of the prestigious Theodore von Kármán award received by Prof. Ruth Nussinov, a minisymposium will be held in her honor, on Oct 22nd at the University of Aachen, in Germany. MarcoDV will present at the minisymposium.
In the occasion of the prestigious Theodore von Kármán award received by Prof. Ruth Nussinov, a minisymposium will be held in her honor, on Oct 22nd at the University of Aachen, in Germany. MarcoDV will present at the minisymposium.
October 2015
MarcoDV is invited to give a talk at the Dept of Chemistry of the University of Padua, Italy, on Oct 8th.
September 2015
MarcoDV is presenting at the FisMat 2015 conference, held at the University of Palermo, Italy.
September 2015
Our conference on computationally-driven drug discovery is getting started!
Ready for the "Computational Advances in Drug Discovery" conference at EPFL in Lausanne!
MarcoDV is invited to give a talk at the Dept of Chemistry of the University of Padua, Italy, on Oct 8th.
September 2015
MarcoDV is presenting at the FisMat 2015 conference, held at the University of Palermo, Italy.
September 2015
Our conference on computationally-driven drug discovery is getting started!
Ready for the "Computational Advances in Drug Discovery" conference at EPFL in Lausanne!
September 2015
MarcoDV is invited speaker at the CECAM workshop entitled "Computational approaches to chemical senses" held on September 9-11, 2015 at CECAM-DE-JUELICH.
August 2015
MarcoDV is presenting at the 250th ACS mtg in Boston at the Drug Discovery session of the COMP division.
MarcoDV is invited speaker at the CECAM workshop entitled "Computational approaches to chemical senses" held on September 9-11, 2015 at CECAM-DE-JUELICH.
August 2015
MarcoDV is presenting at the 250th ACS mtg in Boston at the Drug Discovery session of the COMP division.
July 2015
- MarcoDV joins the Forschungszentrum Jülich (Germany) !
MarcoDV is now also affiliated as Research Associate to the IAS-5 / INM-9 Computational Biomedicine Institute at the Forschungszentrum Jülich (Germany), directed by Prof. P. Carloni.
MarcoDV joins the Translational Medicinal Chemistry team assembled at IAS-5 / INM-9
------------
- One new paper out on Topoisomerase inhibition !
We report combined computational-experimental analyses that explain and quantify the spermine-vectorized F14512’s boosted potency as a topoII poison. F14512 is a compound currently in clinical trials to cure cancer.
This work is the result of a collaboration with the groups of Prof. C. Sissi (University of Padua) and Prof. A. Minarini (University of Bologna).
Read more in:
G. Palermo, E. Minniti, M. L. Greco, L. Riccardi, E. Simoni, M. Convertino, C. Marchetti, M. Rosini, C. Sissi, A. Minarini, M. De Vivo*
"An optimized polyamine moiety boosts potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512"
Chemical Communications, 2015, (Link)
------------
- MarcoDV is Keynote speaker at the CHITEL 2015, the Congress of Theoretical Chemists of Latin Expression which is held in Turin on 26-31 July.
- MarcoDV joins the Forschungszentrum Jülich (Germany) !
MarcoDV is now also affiliated as Research Associate to the IAS-5 / INM-9 Computational Biomedicine Institute at the Forschungszentrum Jülich (Germany), directed by Prof. P. Carloni.
MarcoDV joins the Translational Medicinal Chemistry team assembled at IAS-5 / INM-9
------------
- One new paper out on Topoisomerase inhibition !
We report combined computational-experimental analyses that explain and quantify the spermine-vectorized F14512’s boosted potency as a topoII poison. F14512 is a compound currently in clinical trials to cure cancer.
This work is the result of a collaboration with the groups of Prof. C. Sissi (University of Padua) and Prof. A. Minarini (University of Bologna).
Read more in:
G. Palermo, E. Minniti, M. L. Greco, L. Riccardi, E. Simoni, M. Convertino, C. Marchetti, M. Rosini, C. Sissi, A. Minarini, M. De Vivo*
"An optimized polyamine moiety boosts potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512"
Chemical Communications, 2015, (Link)
------------
- MarcoDV is Keynote speaker at the CHITEL 2015, the Congress of Theoretical Chemists of Latin Expression which is held in Turin on 26-31 July.
June 2015
- One new paper out!
In this paper published on PLoS Comput Biol, we present a new structural enzymatic framework to regulate substrate specificity in lipid-degrading enzymes such as fatty acid amide hydrolase (FAAH).
Read more in:
“Keys to lipid selection in FAAH catalysis: Structural flexibility, gating residues and multiple binding pockets”
PLoS Comput Biol, 2015, 11(6): e1004231 (Link)
This paper is now on the cover of PLoS Comput Biol, with the image of the June issue (Link)
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- Two talks from our PhD students:
Josephine has been selected to present at the school "CHEMICAL AND GENOMICS-BASED STRATEGIES IN THE DISCOVERY OF NOVEL DRUG TARGETS" (22-26 June) at the University of Bologna. Her talk will be on "Understanding protein kinases regulation through computational methods."
Vito will present at the forthcoming CECAM workshop on Modeling Activity vs. Selectivity in Metalloproteins, in Paris.
May 2015
Two new publications!
here, our Essay on the Encyclopedia of Nanotechnology, Springer - we talk about computational methods for drug discovery.
And here, it is where we provide a series of nice examples where computational chemistry has tackled challenging problems related to drug design - published in Volume 1 of the eBooks series entitled, “Frontiers in Computational Chemistry”.
May 2015
MarcoDV has been invited to deliver a lecture on computational methods for drug discovery at the University of Bologna, Dept. of Pharmacy in Rimini, IT.
April 2015
MarcoDV has been invited to deliver a lecture on computational methods for drug discovery at the Institute of Bioengineering, EPFL, Lausanne, CH.
April 2015
OUTREACHING ACTIVITIES: an interview on our research - which is in part supported by the Italian Association for Cancer Research (Associazione Italiana per la Ricerca sul Cancro, or AIRC), here
March 2015
As part of our OUTREACHING ACTIVITIES, it is a great pleasure to report here an article - written by the journalist Federico Mereta - that has been published on Sunday March, 8 2015 on Nova - Il Sole 24 Ore (an Italian daily newspaper). This article mostly describes the use of supercomputers for the study of pharmaceutically relevant targets, and it relates to our recent article published on the Accounts of Chemical Research.: Click here to read the article on Nova
Also, we have had the pleasure to support a fundraising campaign of AIRC and appear on IL Secolo XIX on Friday March, 6 2015:
Click here to read the article
- One new paper out!
In this paper published on PLoS Comput Biol, we present a new structural enzymatic framework to regulate substrate specificity in lipid-degrading enzymes such as fatty acid amide hydrolase (FAAH).
Read more in:
“Keys to lipid selection in FAAH catalysis: Structural flexibility, gating residues and multiple binding pockets”
PLoS Comput Biol, 2015, 11(6): e1004231 (Link)
This paper is now on the cover of PLoS Comput Biol, with the image of the June issue (Link)
--------
- Two talks from our PhD students:
Josephine has been selected to present at the school "CHEMICAL AND GENOMICS-BASED STRATEGIES IN THE DISCOVERY OF NOVEL DRUG TARGETS" (22-26 June) at the University of Bologna. Her talk will be on "Understanding protein kinases regulation through computational methods."
Vito will present at the forthcoming CECAM workshop on Modeling Activity vs. Selectivity in Metalloproteins, in Paris.
May 2015
Two new publications!
here, our Essay on the Encyclopedia of Nanotechnology, Springer - we talk about computational methods for drug discovery.
And here, it is where we provide a series of nice examples where computational chemistry has tackled challenging problems related to drug design - published in Volume 1 of the eBooks series entitled, “Frontiers in Computational Chemistry”.
May 2015
MarcoDV has been invited to deliver a lecture on computational methods for drug discovery at the University of Bologna, Dept. of Pharmacy in Rimini, IT.
April 2015
MarcoDV has been invited to deliver a lecture on computational methods for drug discovery at the Institute of Bioengineering, EPFL, Lausanne, CH.
April 2015
OUTREACHING ACTIVITIES: an interview on our research - which is in part supported by the Italian Association for Cancer Research (Associazione Italiana per la Ricerca sul Cancro, or AIRC), here
March 2015
As part of our OUTREACHING ACTIVITIES, it is a great pleasure to report here an article - written by the journalist Federico Mereta - that has been published on Sunday March, 8 2015 on Nova - Il Sole 24 Ore (an Italian daily newspaper). This article mostly describes the use of supercomputers for the study of pharmaceutically relevant targets, and it relates to our recent article published on the Accounts of Chemical Research.: Click here to read the article on Nova
Also, we have had the pleasure to support a fundraising campaign of AIRC and appear on IL Secolo XIX on Friday March, 6 2015:
Click here to read the article
February 2015
MarcoDV has been invited to deliver a plenary lecture on multiscale modeling of pharmaceutically relevant targets at the Computationally Driven Drug Discovery Meeting (CDDD 4th Meeting), which will be held on February 24-26 at the Auditorium of Angelini Research Center, Santa Palomba, Pomezia (Rome, Italy) - Link
January 2015
A new paper from our group: Our article on mechanistic insights of two-metal-ion catalysis of pharmaceutically relevant enzymes has been accepted on Accounts of Chemical Research - Check here
December 2014
OUTREACHING ACTIVITIES !
Our group on the news - Click here:
News 1: Video abstract of an interview in TV on our research activity
News 2: Interview on the use of World Community Grid to fight Ebola on heatldesk.it
News 3: Interview on the use of World Community Grid to fight Ebola on linkiesta.it
November 2014
MarcoDV, together with Walter Rocchia and Andrea Cavalli, is co-organizying the CECAM workshop entitled "Advance modeling to investigate biomolecules", which is held in IIT on November 20-21, 2014.
Check it out:
http://www.cecam.org/workshop-1137.html
November 2014
Elirosa Minniti joins our group as a PhD student in medicinal chemistry (University of Bologna). Elirosa will work on a project for anticancer drug discovery that is carried out by MarcoDV (IIT) in collaboration with Prof. Anna Minarini (University of Bologna), co-supervisiors of Elirosa, who has been awarded a fellowship from IIT.
Congratulations Elirosa!
November 2014
The John von Neumann Institute for Computing (NIC) granted 300,000 core-h on JUROPA supercomputer at the Jülich Supercomputing Centre (JSC) to the group of Prof. Paolo Carloni, for a project in collaboration with Vito Genna and MarcoDV. The project is focused on QM/MM simulations to decipher how pharmaceutically relevant metallo-enzymes work.
October 2014
Vito Genna, PhD student in our group, has been awarded the prestigious Marco Polo fellowship from the University of Bologna. This fellowship is awarded to outstanding research projects, and will partially cover the expenses related to the period that Vito is spending at the German Research School for Simulation Sciences GmbH, in the group of Prof. Paolo Carloni.
Congratulations Vito!
October 2014
MarcoDV has been invited to visit the Department of Chemistry of the "Universidad de Los Andes" in Bogota, Colombia - where he will deliver lectures on October, 29th and 30th.
September 2014
Two new papers from our group:
Our manuscript on the mechanism for anandamide hydrolysis in FAAH, which proposes a novel dual strategy for efficient enzyme-assisted amide bond cleavage via nitrogen inversion, has been accepted on J. Phys. Chem. B Check here
Also, our review on computational insights into function and inhibition of Fatty Acid Amide Hydrolase has been published on Eur. J. Med. Chem. Check here
September 2014
Marco Borgogno, undergraduate student in Biothechnology at the University of Genoa, joined our group to carry on his research work for his Thesis. He will stay with us ~1 year, working in the wet lab on the synthesis of promising anti-cancer compounds. Welcome Marco!
September 2014
MarcoDV has been invited to deliver a Key Lecture for the session on "Chemistry of Biological Systems", at the XXV National Congress of the Italian Chemical Society, held in Rende (CS, Italy) on Sept 7-12, 2014.
August 2014
MarcoDV will be presenting two talks at the forthcoming 248th ACS meeting in San Francisco, August 10-14.
He will present the recent work on catalysis of the enzyme FAAH, which we have investigated through classical MD and first-principles-based QM/MM simulations, integrated with mutagenesis and kinetic experiments.
This project is in collaboration with Prof. Ursula Rothlisberger, EPFL-Lausanne.
June, 2014
MarcoDV has been invited to lecture on "Computational Chemistry for Drug Discovery" at the International Summer School for PhD Students on "Functional Genomics and Drug Discovery", which is held on June 23-27 at the University of Bologna, Italy.
June, 2014
Jose M. Arencibia (Pepe) joined our group from the Research Group Phosphosites at the J.W. Goethe University Hospital of Frankfurt.
He is a senior postdoc with extensive experience in both in vitro and in vivo molecular biology for anticancer drug discovery.
Pepe will be focused on the evaluation and preliminary characterization of the activity of our most promising anticancer small molecules - in collaboration also with external partners.
Welcome Pepe!
April, 2014
MarcoDV will be lecturing on structure-based drug design and drug discovery at the EPFL-Lausanne, at the Institute of Bioengineering.
Feb, 2014
Our group received 13,9 million core hours from the 8th PRACE Call for proposals (PRACE - Partnership for advanced computing in Europe). This is the second Tier-0 project awarded to our group by PRACE.
Project title: “Lipid degradation in the endocannabinoid system: Deciphering specificity in FAAH catalysis”
PI: Marco De Vivo
Granted: 13,900,000 core hours on CURIE FN (GENCI@CEA, France) – Tier-0 project
Check for more information, here:
http://www.prace-ri.eu
Jan, 2014
Vito Genna, PhD student in our group, is attending the CECAM School MolSim2014, a 2-week school in the field of molecular simulation - held in Amsterdam (January 6-17).
Check out here for more info: MolSim2014
Dec, 2013
The Italian Association for Cancer Research (Associazione Italiana per la Ricerca sul Cancro, or AIRC) has awarded the prestigious "My First AIRC" (MFAG) grant to MarcoDV (PI of the funded project, 2014-2017).
We are grateful to AIRC for the support.
Dec, 2013
Starting from January 2014, Josephine La Sala will be a PhD student at the University of Bologna, and she will carry on her PhD research in "Biochemistry and Biotechnology" in our group. She has been awarded a fellowship from IIT.
Congratulations Josephine!
Nov, 2013
Starting from January 2014, Vito Genna will be a PhD student at the University of Bologna, and he will carry on his PhD research in "Biochemistry and Biotechnology" in our group. He has been awarded a fellowship from IIT.
Congratulations Vito!
Oct, 2013
After the CECAM workshop co-organized in 2011, MarcoDV is now co-organizing a new workshop on “Innovative Aprroaches to Computational Drug Discovery”, at CECAM in Lausanne (EPFL).
Check it out:
Visit “Innovative Aprroaches to Computational Drug Discovery” CECAM workshop
Oct, 2013
Giulia Palermo, who worked under my supervision to obtain her PhD, has just moved to Lausanne for her postdoc, joining the group of Prof. Ursula Rothlisberger at the Dept. of Chemistry - EPFL.
Congratulations Giulia!
Oct, 2013
Jose Antonio Ortega Martínez (Tony) joined our group. He is a senior postdoc in medicinal chemistry, who will be involved in a couple of drug discovery programs.
Welcome Tony!
Sept 2013
MarcoDV is invited speaker at the CECAM workshop: "Coupling between protein, water, and lipid dynamics in complex biological systems: Theory and Experiments." - Lausanne
Sept, 2013
Vito Genna joined our group as Fellow. He will be mainly focused on metalloenzyme catalysis and inhibition.
Welcome Vito!
Sept, 2013
Laura Riccardi joined our group as a junior postdoc, after receiving her PhD in Germany, in the group of Dr. Gerhard Stock, Goethe University of Frankfurt.
She will be mainly focused on metalloenzyme catalysis and inhibition.
Welcome Laura!
April, 2013
Giulia Palermo defended her PhD Thesis, and received her PhD in drug discovery. Giulia performed her PhD research under my supervision. Giulia will move soon to Lausanne for her postdoc, joining the group of Prof. Ursula Rothlisberger at the Dept. of Chemistry - EPFL.
Congratulations Giulia!
MarcoDV has been invited to deliver a plenary lecture on multiscale modeling of pharmaceutically relevant targets at the Computationally Driven Drug Discovery Meeting (CDDD 4th Meeting), which will be held on February 24-26 at the Auditorium of Angelini Research Center, Santa Palomba, Pomezia (Rome, Italy) - Link
January 2015
A new paper from our group: Our article on mechanistic insights of two-metal-ion catalysis of pharmaceutically relevant enzymes has been accepted on Accounts of Chemical Research - Check here
December 2014
OUTREACHING ACTIVITIES !
Our group on the news - Click here:
News 1: Video abstract of an interview in TV on our research activity
News 2: Interview on the use of World Community Grid to fight Ebola on heatldesk.it
News 3: Interview on the use of World Community Grid to fight Ebola on linkiesta.it
November 2014
MarcoDV, together with Walter Rocchia and Andrea Cavalli, is co-organizying the CECAM workshop entitled "Advance modeling to investigate biomolecules", which is held in IIT on November 20-21, 2014.
Check it out:
http://www.cecam.org/workshop-1137.html
November 2014
Elirosa Minniti joins our group as a PhD student in medicinal chemistry (University of Bologna). Elirosa will work on a project for anticancer drug discovery that is carried out by MarcoDV (IIT) in collaboration with Prof. Anna Minarini (University of Bologna), co-supervisiors of Elirosa, who has been awarded a fellowship from IIT.
Congratulations Elirosa!
November 2014
The John von Neumann Institute for Computing (NIC) granted 300,000 core-h on JUROPA supercomputer at the Jülich Supercomputing Centre (JSC) to the group of Prof. Paolo Carloni, for a project in collaboration with Vito Genna and MarcoDV. The project is focused on QM/MM simulations to decipher how pharmaceutically relevant metallo-enzymes work.
October 2014
Vito Genna, PhD student in our group, has been awarded the prestigious Marco Polo fellowship from the University of Bologna. This fellowship is awarded to outstanding research projects, and will partially cover the expenses related to the period that Vito is spending at the German Research School for Simulation Sciences GmbH, in the group of Prof. Paolo Carloni.
Congratulations Vito!
October 2014
MarcoDV has been invited to visit the Department of Chemistry of the "Universidad de Los Andes" in Bogota, Colombia - where he will deliver lectures on October, 29th and 30th.
September 2014
Two new papers from our group:
Our manuscript on the mechanism for anandamide hydrolysis in FAAH, which proposes a novel dual strategy for efficient enzyme-assisted amide bond cleavage via nitrogen inversion, has been accepted on J. Phys. Chem. B Check here
Also, our review on computational insights into function and inhibition of Fatty Acid Amide Hydrolase has been published on Eur. J. Med. Chem. Check here
September 2014
Marco Borgogno, undergraduate student in Biothechnology at the University of Genoa, joined our group to carry on his research work for his Thesis. He will stay with us ~1 year, working in the wet lab on the synthesis of promising anti-cancer compounds. Welcome Marco!
September 2014
MarcoDV has been invited to deliver a Key Lecture for the session on "Chemistry of Biological Systems", at the XXV National Congress of the Italian Chemical Society, held in Rende (CS, Italy) on Sept 7-12, 2014.
August 2014
MarcoDV will be presenting two talks at the forthcoming 248th ACS meeting in San Francisco, August 10-14.
He will present the recent work on catalysis of the enzyme FAAH, which we have investigated through classical MD and first-principles-based QM/MM simulations, integrated with mutagenesis and kinetic experiments.
This project is in collaboration with Prof. Ursula Rothlisberger, EPFL-Lausanne.
June, 2014
MarcoDV has been invited to lecture on "Computational Chemistry for Drug Discovery" at the International Summer School for PhD Students on "Functional Genomics and Drug Discovery", which is held on June 23-27 at the University of Bologna, Italy.
June, 2014
Jose M. Arencibia (Pepe) joined our group from the Research Group Phosphosites at the J.W. Goethe University Hospital of Frankfurt.
He is a senior postdoc with extensive experience in both in vitro and in vivo molecular biology for anticancer drug discovery.
Pepe will be focused on the evaluation and preliminary characterization of the activity of our most promising anticancer small molecules - in collaboration also with external partners.
Welcome Pepe!
April, 2014
MarcoDV will be lecturing on structure-based drug design and drug discovery at the EPFL-Lausanne, at the Institute of Bioengineering.
Feb, 2014
Our group received 13,9 million core hours from the 8th PRACE Call for proposals (PRACE - Partnership for advanced computing in Europe). This is the second Tier-0 project awarded to our group by PRACE.
Project title: “Lipid degradation in the endocannabinoid system: Deciphering specificity in FAAH catalysis”
PI: Marco De Vivo
Granted: 13,900,000 core hours on CURIE FN (GENCI@CEA, France) – Tier-0 project
Check for more information, here:
http://www.prace-ri.eu
Jan, 2014
Vito Genna, PhD student in our group, is attending the CECAM School MolSim2014, a 2-week school in the field of molecular simulation - held in Amsterdam (January 6-17).
Check out here for more info: MolSim2014
Dec, 2013
The Italian Association for Cancer Research (Associazione Italiana per la Ricerca sul Cancro, or AIRC) has awarded the prestigious "My First AIRC" (MFAG) grant to MarcoDV (PI of the funded project, 2014-2017).
We are grateful to AIRC for the support.
Dec, 2013
Starting from January 2014, Josephine La Sala will be a PhD student at the University of Bologna, and she will carry on her PhD research in "Biochemistry and Biotechnology" in our group. She has been awarded a fellowship from IIT.
Congratulations Josephine!
Nov, 2013
Starting from January 2014, Vito Genna will be a PhD student at the University of Bologna, and he will carry on his PhD research in "Biochemistry and Biotechnology" in our group. He has been awarded a fellowship from IIT.
Congratulations Vito!
Oct, 2013
After the CECAM workshop co-organized in 2011, MarcoDV is now co-organizing a new workshop on “Innovative Aprroaches to Computational Drug Discovery”, at CECAM in Lausanne (EPFL).
Check it out:
Visit “Innovative Aprroaches to Computational Drug Discovery” CECAM workshop
Oct, 2013
Giulia Palermo, who worked under my supervision to obtain her PhD, has just moved to Lausanne for her postdoc, joining the group of Prof. Ursula Rothlisberger at the Dept. of Chemistry - EPFL.
Congratulations Giulia!
Oct, 2013
Jose Antonio Ortega Martínez (Tony) joined our group. He is a senior postdoc in medicinal chemistry, who will be involved in a couple of drug discovery programs.
Welcome Tony!
Sept 2013
MarcoDV is invited speaker at the CECAM workshop: "Coupling between protein, water, and lipid dynamics in complex biological systems: Theory and Experiments." - Lausanne
Sept, 2013
Vito Genna joined our group as Fellow. He will be mainly focused on metalloenzyme catalysis and inhibition.
Welcome Vito!
Sept, 2013
Laura Riccardi joined our group as a junior postdoc, after receiving her PhD in Germany, in the group of Dr. Gerhard Stock, Goethe University of Frankfurt.
She will be mainly focused on metalloenzyme catalysis and inhibition.
Welcome Laura!
April, 2013
Giulia Palermo defended her PhD Thesis, and received her PhD in drug discovery. Giulia performed her PhD research under my supervision. Giulia will move soon to Lausanne for her postdoc, joining the group of Prof. Ursula Rothlisberger at the Dept. of Chemistry - EPFL.
Congratulations Giulia!
