Discrete molecular dynamics
Overview
Elizabeth A. Proctor, Feng Ding, Nikolay V. Dokholyan
Published Online: Jan 21 2011
DOI:10.1002/wcms.4
How to cite this WIREs title:
WIREs Comput Mol Sci
WIREs Comput Mol Sci
Impact Factor: 16.778
Molecular and Statistical Mechanics
Gaussian accelerated molecular dynamics: Principles and applications
Advanced Review
Jinan Wang, Pablo R. Arantes, Apurba Bhattarai, Rohaine V. Hsu, Shristi Pawnikar, Yu‐ming M. Huang, Giulia Palermo, Yinglong Miao
Published Online: Mar 02 2021
DOI:10.1002/wcms.1521
Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials
Focus Article
Jorge Nochebuena, Sehr Naseem‐Khan, G. Andrés Cisneros
Published Online: Jan 12 2021
DOI:10.1002/wcms.1515
Modeling molecular kinetics with Milestoning
Advanced Review
Ron Elber, Arman Fathizadeh, Piao Ma, Hao Wang
Published Online: Dec 18 2020
DOI:10.1002/wcms.1512
The challenge of predicting distal active site mutations in computational enzyme design
Advanced Review
Sílvia Osuna
Published Online: Aug 25 2020
DOI:10.1002/wcms.1502
First‐principles dynamics of photoexcited molecules and materials towards a quantum description
Advanced Review
Peiwei You, Daqiang Chen, Chao Lian, Cui Zhang, Sheng Meng
Published Online: Jul 20 2020
DOI:10.1002/wcms.1492
Structural prediction of protein interactions and docking using conservation and coevolution
Advanced Review
Jessica Andreani, Chloé Quignot, Raphael Guerois
Published Online: May 02 2020
DOI:10.1002/wcms.1470
P2Y1‐like nucleotide receptors—Structures, molecular modeling, mutagenesis, and oligomerization
Overview
Vigneshwaran Namasivayam, Christa E. Müller, Alexander Neumann
Published Online: Mar 03 2020
DOI:10.1002/wcms.1464
Next generation 3D pharmacophore modeling
Advanced Review
Gerhard Wolber, Marcel Bermudez, David Machalz, Szymon Pach, Trung Ngoc Nguyen, Lihua Deng, Theresa Noonan, Dora Šribar, David Schaller
Published Online: Feb 26 2020
DOI:10.1002/wcms.1468
Generalized Kohn‐Sham energy decomposition analysis and its applications
Advanced Review
Wei Wu, Zhen Tang, Peifeng Su
Published Online: Jan 13 2020
DOI:10.1002/wcms.1460
Ligand binding free energy and kinetics calculation in 2020
Advanced Review
Vittorio Limongelli
Published Online: Jan 09 2020
DOI:10.1002/wcms.1455
Information‐theoretic approach in density functional theory and its recent applications to chemical problems
Focus Article
Chunying Rong, Bin Wang, Dongbo Zhao, Shubin Liu
Published Online: Dec 30 2019
DOI:10.1002/wcms.1461
Recent developments in symmetry‐adapted perturbation theory
Advanced Review
Konrad Patkowski
Published Online: Nov 28 2019
DOI:10.1002/wcms.1452
Surviving the deluge of biosimulation data
Advanced Review
Adam Hospital, Federica Battistini, Robert Soliva, Josep Lluis Gelpí, Modesto Orozco
Published Online: Nov 21 2019
DOI:10.1002/wcms.1449
A modern challenge of polymer physics: Novel ways to study, interpret, and reconstruct chromatin structure
Advanced Review
Andrea M. Chiariello, Francesco Musella, Renato Sciarretta, Mattia Conte, Andrea Esposito, Simona Bianco, Luca Fiorillo
Published Online: Nov 16 2019
DOI:10.1002/wcms.1454
Computational prediction of protein–protein binding affinities
Advanced Review
Martin Zacharias, Till Siebenmorgen
Published Online: Oct 29 2019
DOI:10.1002/wcms.1448
Classical molecular dynamics on graphics processing unit architectures
Overview
Ádám Jász, Ádám Rák, István Ladjánszki, György Cserey
Published Online: Sep 05 2019
DOI:10.1002/wcms.1444
Hybrid discrete‐continuum solvation methods
Advanced Review
Jose M. Riveros, Josefredo R. Pliego
Published Online: Aug 04 2019
DOI:10.1002/wcms.1440
Surface hopping methods for nonadiabatic dynamics in extended systems
Advanced Review
Linjun Wang, Jing Qiu, Xin Bai, Jiabo Xu
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
Jin Zhao, Xiang Jiang, Yanan Wang, Hongli Guo, Lili Zhang, Chuanyu Zhao, Weibin Chu, Qijing Zheng
Published Online: Mar 14 2019
DOI:10.1002/wcms.1411
Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?
Advanced Review
Cunliang Geng, Li C. Xue, Jorge Roel‐Touris, Alexandre M. J. J. Bonvin
Published Online: Jan 15 2019
DOI:10.1002/wcms.1410
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
Glutamine synthetase structure‐catalysis relationship—Recent advances and applications
Overview
Pedro Manuel Azevedo Alexandrino Fernandes, Maria João Ribeiro Nunes Ramos, Cátia Daniela dos Santos Moreira
Published Online: Nov 22 2018
DOI:10.1002/wcms.1399
Molecular dynamics simulations of macromolecular crystals
Advanced Review
David S. Cerutti, David A. Case
Published Online: Nov 16 2018
DOI:10.1002/wcms.1402
Exploring high‐dimensional free energy landscapes of chemical reactions
Focus Article
Shalini Awasthi, Nisanth N. Nair
Published Online: Nov 16 2018
DOI:10.1002/wcms.1398
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
Disassembling solvation free energies into local contributions—Toward a microscopic understanding of solvation processes
Advanced Review
Matthias Heyden
Published Online: Aug 30 2018
DOI:10.1002/wcms.1390
Reactive molecular dynamics: From small molecules to proteins
Advanced Review
Markus Meuwly
Published Online: Aug 24 2018
DOI:10.1002/wcms.1386
On flexible force fields for metal–organic frameworks: Recent developments and future prospects
Advanced Review
Jurn Heinen, David Dubbeldam
Published Online: Mar 25 2018
DOI:10.1002/wcms.1363
Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment
Advanced Review
Damien Thompson, Liang Xu, Shayon Bhattacharya
Published Online: Feb 13 2018
DOI:10.1002/wcms.1359
Molecular simulations in drug delivery: Opportunities and challenges
Advanced Review
Ratna S. Katiyar, Prateek K. Jha
Published Online: Feb 01 2018
DOI:10.1002/wcms.1358
Advanced models for water simulations
Advanced Review
Omar Demerdash, Lee‐Ping Wang, Teresa Head‐Gordon
Published Online: Nov 23 2017
DOI:10.1002/wcms.1355
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
Interaction entropy for computational alanine scanning in protein–protein binding
Overview
Linqiong Qiu, Yuna Yan, Zhaoxi Sun, Jianing Song, John Z.H. Zhang
Published Online: Oct 24 2017
DOI:10.1002/wcms.1342
Reaction coordinates and transition states in enzymatic catalysis
Advanced Review
Kirill Zinovjev, Iñaki Tuñón
Published Online: Sep 04 2017
DOI:10.1002/wcms.1329
Integrative approaches in HIV‐1 non‐nucleoside reverse transcriptase inhibitor design
Overview
Vasanthanathan Poongavanam, Vigneshwaran Namasivayam, Murugesan Vanangamudi, Hadi Al Shamaileh, Rakesh N Veedu, Jan Kihlberg, N Arul Murugan
Published Online: Aug 30 2017
DOI:10.1002/wcms.1328
Recent advances in dynamic docking for drug discovery
Opinion
Marco De Vivo, Andrea Cavalli
Published Online: Jun 13 2017
DOI:10.1002/wcms.1320
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
Molecular ‘time‐machines’ to unravel key biological events for drug design
Overview
Aravindhan Ganesan, Michelle L. Coote, Khaled Barakat
Published Online: May 02 2017
DOI:10.1002/wcms.1306
Accelerating physical simulations of proteins by leveraging external knowledge
Advanced Review
Ken A. Dill, Joseph A. Morrone, Alberto Perez
Published Online: Apr 19 2017
DOI:10.1002/wcms.1309
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
3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?
Advanced Review
Marc A. Marti‐Renom, François Serra, François Le Dily
Published Online: Apr 10 2017
DOI:10.1002/wcms.1308
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
Using PyMOL as a platform for computational drug design
Software Focus
Zhenquan Hu, H.C. Stephen Chan, Shuguang Yuan
Published Online: Jan 05 2017
DOI:10.1002/wcms.1298
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
What can molecular simulation do for global warming?
Advanced Review
De‐en Jiang, Sheng Dai, Ziqi Tian
Published Online: Jan 21 2016
DOI:10.1002/wcms.1241
Modeling of ribonucleic acid–ligand interactions
Advanced Review
Janusz M. Bujnicki, Wayne K. Dawson, Michael Bodkin, Ewa I. Chudyk, Filip Stefaniak
Published Online: Sep 14 2015
DOI:10.1002/wcms.1226
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
Correct electrostatic treatment of noncovalent interactions: the importance of polarization
Overview
Timothy Clark, Peter Politzer, Jane S. Murray
Published Online: Dec 01 2014
DOI:10.1002/wcms.1210
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
Symmetry‐adapted perturbation theory based on density functional theory for noncovalent interactions
Advanced Review
Georg Jansen
Published Online: Aug 22 2013
DOI:10.1002/wcms.1164
Frontiers in free‐energy calculations of biological systems
Advanced Review
Christophe Chipot
Published Online: Jun 06 2013
DOI:10.1002/wcms.1157
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
The description of electronic processes inside proteins from Car–Parrinello molecular dynamics: chemical transformations
Overview
Carme Rovira
Published Online: May 03 2013
DOI:10.1002/wcms.1153
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
Proteins in the gas phase
Advanced Review
Tim Meyer, Valérie Gabelica, Helmut Grubmüller, Modesto Orozco
Published Online: Nov 29 2012
DOI:10.1002/wcms.1130
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
Recent successes in coarse‐grained modeling of DNA
Advanced Review
Davit A. Potoyan, Alexey Savelyev, Garegin A. Papoian
Published Online: Aug 08 2012
DOI:10.1002/wcms.1114
Coarse‐grained models of water
Overview
Sergio Pantano, Matías R. Machado, Leonardo Darré
Published Online: Jun 06 2012
DOI:10.1002/wcms.1097
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
Carbohydrate force fields
Advanced Review
B. Lachele Foley, Matthew B. Tessier, Robert J. Woods
Published Online: Oct 31 2011
DOI:10.1002/wcms.89
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
Recent developments and applications of the CHARMM force fields
Advanced Review
Xiao Zhu, Pedro E. M. Lopes, Alexander D. MacKerell
Published Online: Jun 28 2011
DOI:10.1002/wcms.74
Selected features of the polarizable continuum model for the representation of solvation
Advanced Review
Jacopo Tomasi
Published Online: Jun 03 2011
DOI:10.1002/wcms.54
Umbrella sampling
Advanced Review
Johannes Kästner
Published Online: May 26 2011
DOI:10.1002/wcms.66
The COSMO and COSMO‐RS solvation models
Advanced Review
Andreas Klamt
Published Online: Apr 28 2011
DOI:10.1002/wcms.56
Proline‐derived organocatalysis and synergism between theory and experiments
Overview
Raghavan B. Sunoj
Published Online: Apr 15 2011
DOI:10.1002/wcms.37
Cation–π and anion–π interactions
Advanced Review
Antonio Frontera, David Quiñonero, Pere M. Deyà
Published Online: Apr 11 2011
DOI:10.1002/wcms.14
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
Metadynamics
Advanced Review
Michele Parrinello, Massimiliano Bonomi, Alessandro Barducci
Published Online: Feb 18 2011
DOI:10.1002/wcms.31
Polarization effects in molecular interactions
Overview
Modesto Orozco, Christophe Chipot, François Dehez, F. Javier Luque
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