M
Martin Zacharias
Researcher at Technische Universität München
Publications - 344
Citations - 11986
Martin Zacharias is an academic researcher from Technische Universität München. The author has contributed to research in topics: Molecular dynamics & Medicine. The author has an hindex of 56, co-authored 304 publications receiving 10109 citations. Previous affiliations of Martin Zacharias include Jacobs University Bremen & International University, Cambodia.
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Journal ArticleDOI
Separation‐shifted scaling, a new scaling method for Lennard‐Jones interactions in thermodynamic integration
TL;DR: In this paper, a new method of simultaneously scaling and shifting the LJ potential in molecular dynamics and thermodynamic integration (TI) simulations is presented, which allows the smooth creation or annihilation of atoms or molecules in an ensemble of solvent molecules during a molecular simulation.
Journal ArticleDOI
NWChem: Past, present, and future
Edoardo Aprà,Eric J. Bylaska,W. A. de Jong,Niranjan Govind,Karol Kowalski,T. P. Straatsma,Marat Valiev,H. J. J. van Dam,Yuri Alexeev,J. Anchell,V. Anisimov,Fredy W. Aquino,Raymond Atta-Fynn,Jochen Autschbach,Nicholas P. Bauman,Jeffrey C. Becca,David E. Bernholdt,K. Bhaskaran-Nair,Stuart Bogatko,Piotr Borowski,Jeffery S. Boschen,Jiří Brabec,Adam Bruner,Emilie Cauet,Y. Chen,Gennady N. Chuev,Christopher J. Cramer,Jeff Daily,M. J. O. Deegan,Thom H. Dunning,Michel Dupuis,Kenneth G. Dyall,George I. Fann,Sean A. Fischer,Alexandr Fonari,Herbert A. Früchtl,Laura Gagliardi,Jorge Garza,Nitin A. Gawande,Soumen Ghosh,Kurt R. Glaesemann,Andreas W. Götz,Jeff R. Hammond,Volkhard Helms,Eric D. Hermes,Kimihiko Hirao,So Hirata,Mathias Jacquelin,Lasse Jensen,Benny G. Johnson,Hannes Jónsson,Ricky A. Kendall,Michael Klemm,Rika Kobayashi,V. Konkov,Sriram Krishnamoorthy,M. Krishnan,Zijing Lin,Roberto D. Lins,Rik J. Littlefield,Andrew J. Logsdail,Kenneth Lopata,Wan Yong Ma,Aleksandr V. Marenich,J. Martin del Campo,Daniel Mejía-Rodríguez,Justin E. Moore,Jonathan M. Mullin,Takahito Nakajima,Daniel R. Nascimento,Jeffrey A. Nichols,P. J. Nichols,J. Nieplocha,Alberto Otero-de-la-Roza,Bruce J. Palmer,Ajay Panyala,T. Pirojsirikul,Bo Peng,Roberto Peverati,Jiri Pittner,L. Pollack,Ryan M. Richard,P. Sadayappan,George C. Schatz,William A. Shelton,Daniel W. Silverstein,D. M. A. Smith,Thereza A. Soares,Duo Song,Marcel Swart,H. L. Taylor,G. S. Thomas,Vinod Tipparaju,Donald G. Truhlar,Kiril Tsemekhman,T. Van Voorhis,Álvaro Vázquez-Mayagoitia,Prakash Verma,Oreste Villa,Abhinav Vishnu,Konstantinos D. Vogiatzis,Dunyou Wang,John H. Weare,Mark J. Williamson,Theresa L. Windus,Krzysztof Wolinski,A. T. Wong,Qin Wu,Chan-Shan Yang,Q. Yu,Martin Zacharias,Zhiyong Zhang,Yan Zhao,Robert W. Harrison +113 more
TL;DR: The NWChem computational chemistry suite is reviewed, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.
Journal ArticleDOI
Protein–protein docking with a reduced protein model accounting for side-chain flexibility
TL;DR: The multicopy approach significantly improves the docking performance, using unbound (apo) binding partners without a significant increase in computer time and could be extended to include protein loop flexibility, and might also be useful for docking of modeled protein structures.
Journal ArticleDOI
NWChem: Past, Present, and Future
Edoardo Aprà,Eric J. Bylaska,W. A. de Jong,Niranjan Govind,Karol Kowalski,T. P. Straatsma,Marat Valiev,H. J. J. van Dam,Yuri Alexeev,James L. Anchell,Victor M. Anisimov,Fredy W. Aquino,Raymond Atta-Fynn,Jochen Autschbach,Nicholas P. Bauman,Jeffrey C. Becca,David E. Bernholdt,Kiran Bhaskaran-Nair,Stuart Bogatko,Piotr Borowski,Jeffrey Scott Boschen,Jiří Brabec,Adam Bruner,Emilie Cauet,Y. Chen,Gennady N. Chuev,Christopher J. Cramer,Jeff Daily,M. J. O. Deegan,Thomas Dunning,Michel Dupuis,Kenneth G. Dyall,George I. Fann,Sean A. Fischer,Alexandr Fonari,H. Früuchtl,Laura Gagliardi,Jorge Garza,Nitin A. Gawande,Sayan Ghosh,Kurt R. Glaesemann,Andreas W. Götz,Jeff R. Hammond,Volkhard Helms,Eric D. Hermes,Kimihiko Hirao,So Hirata,Mathias Jacquelin,Lasse Jensen,Benny G. Johnson,Hannes Jónsson,Ricky A. Kendall,Michael Klemm,Rika Kobayashi,V. Konkov,Sriram Krishnamoorthy,Manojkumar Krishnan,Zijing Lin,Roberto D. Lins,Rik J. Littlefield,Andrew J. Logsdail,Kenneth Lopata,Wan Yong Ma,Aleksandr V. Marenich,J. Martin del Campo,Daniel Mejía-Rodríguez,Justin E. Moore,Jonathan M. Mullin,Takahito Nakajima,Daniel R. Nascimento,Jeffrey A. Nichols,Patrick Nichols,J. Nieplocha,A. Otero de la Roza,Bruce J. Palmer,Ajay Panyala,T. Pirojsirikul,Bo Peng,Roberto Peverati,Jiri Pittner,L. Pollack,Ryan M. Richard,P. Sadayappan,George C. Schatz,William A. Shelton,Daniel W. Silverstein,Dayle M. A. Smith,Thereza A. Soares,Duo Song,Marcel Swart,H. L. Taylor,G. S. Thomas,Vinod Tipparaju,Donald G. Truhlar,Kiril Tsemekhman,T. Van Voorhis,Álvaro Vázquez-Mayagoitia,Prakash Verma,Oreste Villa,Abhinav Vishnu,Konstantinos D. Vogiatzis,Dunyou Wang,John H. Weare,Mark J. Williamson,T. L. Windus,Krzysztof Wolinski,A. T. Wong,Qin Wu,Chan-Shan Yang,Q. Yu,Martin Zacharias,Zhiyong Zhang,Yan Zhao,Robert W. Harrison +113 more
TL;DR: The NWChem computational chemistry suite as discussed by the authors provides tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties by using first-principledriven methodologies to model complex chemical and materials processes.
Journal ArticleDOI
A family of macrodomain proteins reverses cellular mono-ADP-ribosylation
Gytis Jankevicius,Markus Hassler,Barbara Golia,Vladimir Rybin,Martin Zacharias,Gyula Timinszky,Andreas G. Ladurner +6 more
TL;DR: These discoveries establish the complete reversibility of PARP-catalyzed cellular ADP-ribosylation as a regulatory modification and identify a family of macrodomain enzymes present in viruses, yeast and animals that reverse cellular ADp-ribsylation by acting on mono-ADP- ribosylated substrates.