Discrete molecular dynamics
Overview
Elizabeth A. Proctor, Feng Ding, Nikolay V. Dokholyan
Published Online: Jan 21 2011
DOI:10.1002/wcms.4
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Molecular Dynamics and Monte-Carlo Methods
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Molecular Dynamics and Monte-Carlo Methods
Ligand binding free energy and kinetics calculation in 2020
Advanced Review
Vittorio Limongelli
Published Online: Jan 10 2020
DOI:10.1002/wcms.1455
Surviving the deluge of biosimulation data
Advanced Review
Adam Hospital, Federica Battistini, Robert Soliva, Josep Lluis Gelpí, Modesto Orozco
Published Online: Nov 22 2019
DOI:10.1002/wcms.1449
A modern challenge of polymer physics: Novel ways to study, interpret, and reconstruct chromatin structure
Advanced Review
Luca Fiorillo, Simona Bianco, Andrea Esposito, Mattia Conte, Renato Sciarretta, Francesco Musella, Andrea M. Chiariello
Published Online: Nov 16 2019
DOI:10.1002/wcms.1454
Classical molecular dynamics on graphics processing unit architectures
Overview
György Cserey, István Ladjánszki, Ádám Rák, Ádám Jász
Published Online: Sep 05 2019
DOI:10.1002/wcms.1444
Surface hopping methods for nonadiabatic dynamics in extended systems
Advanced Review
Jiabo Xu, Xin Bai, Jing Qiu, Linjun Wang
Published Online: Jul 29 2019
DOI:10.1002/wcms.1435
Recent advances in quantum‐mechanical molecular dynamics simulations of proton transfer mechanism in various water‐based environments
Advanced Review
Aditya W. Sakti, Yoshifumi Nishimura, Hiromi Nakai
Published Online: May 31 2019
DOI:10.1002/wcms.1419
Ab initio nonadiabatic molecular dynamics investigations on the excited carriers in condensed matter systems
Advanced Review
Qijing Zheng, Weibin Chu, Chuanyu Zhao, Lili Zhang, Hongli Guo, Yanan Wang, Xiang Jiang, Jin Zhao
Published Online: Mar 14 2019
DOI:10.1002/wcms.1411
Rationalization of stereoselectivity in enzyme reactions
Advanced Review
H. C. Stephen Chan, Lu Pan, Yi Li, Shuguang Yuan
Published Online: Dec 05 2018
DOI:10.1002/wcms.1403
Molecular dynamics simulations of macromolecular crystals
Advanced Review
David S. Cerutti, David A. Case
Published Online: Nov 16 2018
DOI:10.1002/wcms.1402
Computer‐aided drug design in new druggable targets for the next generation of immune‐oncology therapies
Overview
Rita C. Guedes, Helena F. Florindo, Ronit Satchi‐Fainaro, Anna Scomparin, Rita C. Acúrcio
Published Online: Oct 29 2018
DOI:10.1002/wcms.1397
Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
Overview
Marc W. van der Kamp, Mark S. P. Sansom, Edina Rosta, Adrian J. Mulholland, Julien Michel, Charles A. Laughton, Antonija Kuzmanic, Syma Khalid, Richard H. Henchman, Sarah A. Harris, Jonathan W. Essex, Marc A. Dämgen, Philip C. Biggin, David J. Huggins
Published Online: Sep 27 2018
DOI:10.1002/wcms.1393
Perspective on computational simulations of glycosaminoglycans
Overview
Balaji Nagarajan, Nehru Viji Sankaranarayanan, Umesh R. Desai
Published Online: Sep 10 2018
DOI:10.1002/wcms.1388
Reactive molecular dynamics: From small molecules to proteins
Advanced Review
Markus Meuwly
Published Online: Aug 24 2018
DOI:10.1002/wcms.1386
Molecular simulations in drug delivery: Opportunities and challenges
Advanced Review
Prateek K. Jha, Ratna S. Katiyar
Published Online: Feb 01 2018
DOI:10.1002/wcms.1358
Atomistic modeling of graphene/hexagonal boron nitride polymer nanocomposites: a review
Advanced Review
Akarsh Verma, Avinash Parashar, M. Packirisamy
Published Online: Nov 13 2017
DOI:10.1002/wcms.1346
Water models for biomolecular simulations
Advanced Review
Saeed Izadi, Alexey V. Onufriev
Published Online: Nov 13 2017
DOI:10.1002/wcms.1347
Protein design: from computer models to artificial intelligence
Advanced Review
Antonella Paladino, Filippo Marchetti, Silvia Rinaldi, Giorgio Colombo
Published Online: May 24 2017
DOI:10.1002/wcms.1318
Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here?
Advanced Review
Adam W. Duster, Chun‐Hung Wang, Christina M. Garza, Danielle E. Miller, Hai Lin
Published Online: Apr 17 2017
DOI:10.1002/wcms.1310
Computational protein structure refinement: almost there, yet still so far to go
Advanced Review
Michael Feig
Published Online: Mar 28 2017
DOI:10.1002/wcms.1307
Organic–inorganic interface simulation for new material discoveries
Overview
Sathish Kumar Ramakrishnan, Jie Zhu, Csilla Gergely
Published Online: Sep 01 2016
DOI:10.1002/wcms.1277
Adaptive quantum mechanics/molecular mechanics methods
Advanced Review
Min Zheng, Mark P. Waller
Published Online: Apr 28 2016
DOI:10.1002/wcms.1255
Computational close up on protein–protein interactions: how to unravel the invisible using molecular dynamics simulations?
Advanced Review
Christin Rakers, Marcel Bermudez, Bettina G. Keller, Jérémie Mortier, Gerhard Wolber
Published Online: Jul 27 2015
DOI:10.1002/wcms.1222
GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
Software Focus
Jaewoon Jung, Takaharu Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, Yuji Sugita
Published Online: May 07 2015
DOI:10.1002/wcms.1220
Polarizable force fields for molecular dynamics simulations of biomolecules
Overview
Christopher M. Baker
Published Online: Jan 26 2015
DOI:10.1002/wcms.1215
Multiresolution calculation of ionic liquids
Overview
Barbara Kirchner, Oldamur Hollóczki, José Nuno Canongia Lopes, Agílio A. H. Pádua
Published Online: Dec 05 2014
DOI:10.1002/wcms.1212
Direct methods for computing single‐molecule entropies from molecular simulations
Advanced Review
Dimas Suárez, Natalia Díaz
Published Online: Jul 25 2014
DOI:10.1002/wcms.1195
Molecular dynamics out of equilibrium: mechanics and measurables
Advanced Review
Rigoberto Hernandez, Alexander V. Popov
Published Online: Jul 15 2014
DOI:10.1002/wcms.1190
Computing protein dynamics from protein structure with elastic network models
Advanced Review
Ugo Bastolla
Published Online: Apr 18 2014
DOI:10.1002/wcms.1186
Predicting enzymatic reactivity: from theory to design
Advanced Review
Katarzyna Świderek, Iñaki Tuñón, Vicent Moliner
Published Online: Oct 08 2013
DOI:10.1002/wcms.1173
Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation
Advanced Review
Christopher M. Baker, Robert B. Best
Published Online: Aug 27 2013
DOI:10.1002/wcms.1167
The power of coarse graining in biomolecular simulations
Advanced Review
Helgi I. Ingólfsson, Cesar A. Lopez, Jaakko J. Uusitalo, Djurre H. de Jong, Srinivasa M. Gopal, Xavier Periole, Siewert J. Marrink
Published Online: Aug 27 2013
DOI:10.1002/wcms.1169
Coarse‐grained methods for polymeric materials: enthalpy‐ and entropy‐driven models
Overview
Paola Carbone, Carlos Avendaño
Published Online: May 10 2013
DOI:10.1002/wcms.1149
High‐throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure
Overview
Adam Hospital, Josep Ll Gelpi
Published Online: Feb 07 2013
DOI:10.1002/wcms.1142
Atomistic simulations of nucleosomes
Overview
Mithun Biswas, Jörg Langowski, Thomas C. Bishop
Published Online: Jan 31 2013
DOI:10.1002/wcms.1139
Predictions of protein–RNA interactions
Advanced Review
Davide Cirillo, Federico Agostini, Gian Gaetano Tartaglia
Published Online: Sep 25 2012
DOI:10.1002/wcms.1119
Resonance energy flow dynamics of coherently delocalized excitons in biological and macromolecular systems: Recent theoretical advances and open issues
Advanced Review
Seogjoo Jang, Yuan‐Chung Cheng
Published Online: Aug 08 2012
DOI:10.1002/wcms.1111
Synergistic use of NMR and MD simulations to study the structural heterogeneity of proteins
Overview
Santiago Esteban‐Martín, Robert Bryn Fenwick, Xavier Salvatella
Published Online: Apr 18 2012
DOI:10.1002/wcms.1093
Optimization of protein models
Advanced Review
Dominik Gront, Sebastian Kmiecik, Maciej Blaszczyk, Dariusz Ekonomiuk, Andrzej Koliński
Published Online: Mar 29 2012
DOI:10.1002/wcms.1090
Electron transfer in DNA
Advanced Review
Khatcharin Siriwong, Alexander A. Voityuk
Published Online: Mar 29 2012
DOI:10.1002/wcms.1102
New advances in metadynamics
Overview
Ludovico Sutto, Simone Marsili, Francesco Luigi Gervasio
Published Online: Mar 29 2012
DOI:10.1002/wcms.1103
Essential dynamics: foundation and applications
Overview
Isabella Daidone, Andrea Amadei
Published Online: Feb 29 2012
DOI:10.1002/wcms.1099
Next challenges in protein–protein docking: from proteome to interactome and beyond
Overview
Adrien S.J. Melquiond, Ezgi Karaca, Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin
Published Online: Sep 28 2011
DOI:10.1002/wcms.91
Umbrella sampling
Advanced Review
Johannes Kästner
Published Online: May 26 2011
DOI:10.1002/wcms.66
Proline‐derived organocatalysis and synergism between theory and experiments
Overview
Raghavan B. Sunoj
Published Online: Apr 15 2011
DOI:10.1002/wcms.37
Cooperative dynamics of proteins unraveled by network models
Overview
Eran Eyal, Anindita Dutta, Ivet Bahar
Published Online: Apr 11 2011
DOI:10.1002/wcms.44
Receptor flexibility in small‐molecule docking calculations
Advanced Review
Daria B. Kokh, Rebecca C. Wade, Wolfgang Wenzel
Published Online: Mar 17 2011
DOI:10.1002/wcms.29
Polarization effects in molecular interactions
Overview
F. Javier Luque, François Dehez, Christophe Chipot, Modesto Orozco
Published Online: Feb 03 2011
DOI:10.1002/wcms.32
Algorithm improvements for molecular dynamics simulations
Advanced Review
Per Larsson, Berk Hess, Erik Lindahl
Published Online: Jan 21 2011
DOI:10.1002/wcms.3