Home
This Title All WIREs
WIREs RSS Feed
How to cite this WIREs title:
WIREs Comput Mol Sci
Impact Factor: 8.127

Computational Biochemistry and Biophysics

                                        View Less
Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling

Advanced Review
Tamar Schlick, Stephanie Portillo‐Ledesma
Published Online: Aug 06 2019
DOI:10.1002/wcms.1434

Abstract Full article on Wiley Online Library:   HTML | PDF
Learning from nature: Understanding hydrogenase enzyme using computational approach

Advanced Review
Siyao Qiu, Qinye Li, Yongjun Xu, Shaohua Shen, Chenghua Sun
Published Online: May 28 2019
DOI:10.1002/wcms.1422

Abstract Full article on Wiley Online Library:   HTML | PDF
The SMFA program for quantum chemistry calculations on large molecules

Software Focus
Rika Kobayashi, Matthew A. Addicoat, Andrew T.B. Gilbert, Roger D. Amos, Michael A. Collins
Published Online: Mar 01 2019
DOI:10.1002/wcms.1413

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
Molecular dynamics simulations of macromolecular crystals

Advanced Review
David S. Cerutti, David A. Case
Published Online: Nov 16 2018
DOI:10.1002/wcms.1402

Abstract Full article on Wiley Online Library:   HTML | PDF
Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity

Overview
David J. Huggins, Philip C. Biggin, Marc A. Dämgen, Jonathan W. Essex, Sarah A. Harris, Richard H. Henchman, Syma Khalid, Antonija Kuzmanic, Charles A. Laughton, Julien Michel, Adrian J. Mulholland, Edina Rosta, Mark S. P. Sansom, Marc W. van der Kamp
Published Online: Sep 27 2018
DOI:10.1002/wcms.1393

Abstract Full article on Wiley Online Library:   HTML | PDF
Electronic energy transfer in biomacromolecules

Advanced Review
Lorenzo Cupellini, Marina Corbella, Benedetta Mennucci, Carles Curutchet
Published Online: Sep 13 2018
DOI:10.1002/wcms.1392

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
Eukaryotic cell dynamics from crawlers to swimmers

Advanced Review
H. G. Othmer
Published Online: Jul 19 2018
DOI:10.1002/wcms.1376

Abstract Full article on Wiley Online Library:   HTML | PDF
Essentials of de novo protein design: Methods and applications

Advanced Review
Enrique Marcos, Daniel‐Adriano Silva
Published Online: Jul 17 2018
DOI:10.1002/wcms.1374

Abstract Full article on Wiley Online Library:   HTML | PDF
Out‐compute drug side effects: Focus on cytochrome P450 2D6 modeling

Advanced Review
Martin Smieško, Charleen G. Don
Published Online: May 03 2018
DOI:10.1002/wcms.1366

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational structure‐based drug design: Predicting target flexibility

Advanced Review
Victor Guallar, Robert Soliva, Suwipa Saen‐oon, Jelisa Iglesias
Published Online: Apr 29 2018
DOI:10.1002/wcms.1367

Abstract Full article on Wiley Online Library:   HTML | PDF
Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment

Advanced Review
Shayon Bhattacharya, Liang Xu, Damien Thompson
Published Online: Feb 13 2018
DOI:10.1002/wcms.1359

Abstract Full article on Wiley Online Library:   HTML | PDF
The sensing mechanism studies of the fluorescent probes with electronically excited state calculations

Advanced Review
Ke‐Li Han, Guang‐Yue Li
Published Online: Nov 17 2017
DOI:10.1002/wcms.1351

Abstract Full article on Wiley Online Library:   HTML | PDF
Water models for biomolecular simulations

Advanced Review
Saeed Izadi, Alexey V. Onufriev
Published Online: Nov 13 2017
DOI:10.1002/wcms.1347

Abstract Full article on Wiley Online Library:   HTML | PDF
Interaction entropy for computational alanine scanning in protein–protein binding

Overview
John Z.H. Zhang, Jianing Song, Zhaoxi Sun, Yuna Yan, Linqiong Qiu
Published Online: Oct 24 2017
DOI:10.1002/wcms.1342

Abstract Full article on Wiley Online Library:   HTML | PDF
Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules

Advanced Review
Wei Wang, Siqin Cao, Lizhe Zhu, Xuhui Huang
Published Online: Oct 06 2017
DOI:10.1002/wcms.1343

Abstract Full article on Wiley Online Library:   HTML | PDF
Reaction coordinates and transition states in enzymatic catalysis

Advanced Review
Kirill Zinovjev, Iñaki Tuñón
Published Online: Sep 04 2017
DOI:10.1002/wcms.1329

Abstract Full article on Wiley Online Library:   HTML | PDF
Integrative approaches in HIV‐1 non‐nucleoside reverse transcriptase inhibitor design

Overview
N Arul Murugan, Jan Kihlberg, Rakesh N Veedu, Hadi Al Shamaileh, Murugesan Vanangamudi, Vigneshwaran Namasivayam, Vasanthanathan Poongavanam
Published Online: Aug 30 2017
DOI:10.1002/wcms.1328

Abstract Full article on Wiley Online Library:   HTML | PDF
Molecular electrostatic potentials and noncovalent interactions

Overview
Jane S. Murray, Peter Politzer
Published Online: Jul 18 2017
DOI:10.1002/wcms.1326

Abstract Full article on Wiley Online Library:   HTML | PDF
The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

Advanced Review
Dmitri G. Fedorov
Published Online: Jun 20 2017
DOI:10.1002/wcms.1322

Abstract Full article on Wiley Online Library:   HTML | PDF
Recent advances in dynamic docking for drug discovery

Opinion
Marco De Vivo, Andrea Cavalli
Published Online: Jun 13 2017
DOI:10.1002/wcms.1320

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
About P‐glycoprotein: a new drugable domain is emerging from structural data

Focus Article
Ricardo J. Ferreira, Cátia A. Bonito, Maria José U. Ferreira, Daniel J.V.A. dos Santos
Published Online: May 04 2017
DOI:10.1002/wcms.1316

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
Rigidity theory for biomolecules: concepts, software, and applications

Advanced Review
Susanne M.A. Hermans, Christopher Pfleger, Christina Nutschel, Christian A. Hanke, Holger Gohlke
Published Online: Apr 27 2017
DOI:10.1002/wcms.1311

Abstract Full article on Wiley Online Library:   HTML | PDF
Polarizable force field development for lipids and their efficient applications in membrane proteins

Overview
Huiying Chu, Liaoran Cao, Xiangda Peng, Guohui Li
Published Online: Apr 26 2017
DOI:10.1002/wcms.1312

Abstract Full article on Wiley Online Library:   HTML | PDF
Accelerating physical simulations of proteins by leveraging external knowledge

Advanced Review
Alberto Perez, Joseph A. Morrone, Ken A. Dill
Published Online: Apr 19 2017
DOI:10.1002/wcms.1309

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

Overview
Maria João Ramos, Pedro A. Fernandes, Nuno M. F. S. A. Cerqueira, Natércia F. Brás, Rui P. P. Neves, António J. M. Ribeiro, Sérgio Filipe Sousa
Published Online: Sep 01 2016
DOI:10.1002/wcms.1281

Abstract Full article on Wiley Online Library:   HTML | PDF
Optimal reaction coordinates

Advanced Review
Polina V. Banushkina, Sergei V. Krivov
Published Online: Aug 10 2016
DOI:10.1002/wcms.1276

Abstract Full article on Wiley Online Library:   HTML | PDF
Adaptive quantum mechanics/molecular mechanics methods

Advanced Review
Min Zheng, Mark P. Waller
Published Online: Apr 28 2016
DOI:10.1002/wcms.1255

Abstract Full article on Wiley Online Library:   HTML | PDF
Coarse‐grained models for studying protein diffusion along DNA

Advanced Review
Arnab Bhattacherjee, Dana Krepel, Yaakov Levy
Published Online: Apr 27 2016
DOI:10.1002/wcms.1262

Abstract Full article on Wiley Online Library:   HTML | PDF
Atomistic molecular dynamics simulations of ATP‐binding cassette transporters

Overview
Tingjun Hou, Youyong Li, Dan Li, Hui Liu
Published Online: Jan 22 2016
DOI:10.1002/wcms.1247

Abstract Full article on Wiley Online Library:   HTML | PDF
Modeling of ribonucleic acid–ligand interactions

Advanced Review
Filip Stefaniak, Ewa I. Chudyk, Michael Bodkin, Wayne K. Dawson, Janusz M. Bujnicki
Published Online: Sep 14 2015
DOI:10.1002/wcms.1226

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational estimation of pKa values

Overview
Paul G. Seybold, George C. Shields
Published Online: Mar 24 2015
DOI:10.1002/wcms.1218

Abstract Full article on Wiley Online Library:   HTML | PDF
Exploiting the potential energy landscape to sample free energy

Overview
Andrew J. Ballard, Stefano Martiniani, Jacob D. Stevenson, Sandeep Somani, David J. Wales
Published Online: Mar 20 2015
DOI:10.1002/wcms.1217

Abstract Full article on Wiley Online Library:   HTML | PDF
Polarizable force fields for molecular dynamics simulations of biomolecules

Overview
Christopher M. Baker
Published Online: Jan 26 2015
DOI:10.1002/wcms.1215

Abstract Full article on Wiley Online Library:   HTML | PDF
Structural modeling from electron microscopy data

Advanced Review
José Ramón López‐Blanco, Pablo Chacón
Published Online: Sep 15 2014
DOI:10.1002/wcms.1199

Abstract Full article on Wiley Online Library:   HTML | PDF
Software for predicting the 3D structure of RNA molecules

Software Focus
David Dufour, Marc A. Marti‐Renom
Published Online: Sep 09 2014
DOI:10.1002/wcms.1198

Abstract Full article on Wiley Online Library:   HTML | PDF
Reversing cancer multidrug resistance: insights into the efflux by ABC transports from in silico studies

Advanced Review
Ricardo J. Ferreira, Maria‐José U. Ferreira, Daniel J. V. A. dos Santos
Published Online: Aug 18 2014
DOI:10.1002/wcms.1196

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
The many faces of halogen bonding: a review of theoretical models and methods

Advanced Review
Lando P. Wolters, Patric Schyman, Mariela J. Pavan, William L. Jorgensen, F. Matthias Bickelhaupt, Sebastian Kozuch
Published Online: Jun 09 2014
DOI:10.1002/wcms.1189

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
Tautomerism in nucleic acid bases and base pairs: a brief overview

Overview
Manoj K. Shukla, Jerzy Leszczynski
Published Online: Feb 22 2013
DOI:10.1002/wcms.1145

Abstract Full article on Wiley Online Library:   HTML | PDF
Prediction of protein binding sites and hot spots

Advanced Review
Juan Fernández‐Recio
Published Online: May 03 2011
DOI:10.1002/wcms.45

Abstract Full article on Wiley Online Library:   HTML | PDF
The atomistic simulation of DNA

Overview
Charles A. Laughton, Sarah A. Harris
Published Online: Apr 19 2011
DOI:10.1002/wcms.46

Abstract Full article on Wiley Online Library:   HTML | PDF
Outstanding challenges in protein–ligand docking and structure‐based virtual screening

Advanced Review
Bohdan Waszkowycz, David E. Clark, Emanuela Gancia
Published Online: Mar 16 2011
DOI:10.1002/wcms.18

Abstract Full article on Wiley Online Library:   HTML | PDF
The quantum chemical cluster approach for modeling enzyme reactions

Overview
Per E.M. Siegbahn, Fahmi Himo
Published Online: Mar 10 2011
DOI:10.1002/wcms.13

Abstract Full article on Wiley Online Library:   HTML | PDF
Low‐resolution structural approaches to study biomolecular assemblies

Overview
Pau Bernadó
Published Online: Feb 18 2011
DOI:10.1002/wcms.15

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
Mixed quantum mechanics and molecular mechanics methods: Looking inside proteins

Advanced Review
Frank H. Wallrapp, Victor Guallar
Published Online: Feb 01 2011
DOI:10.1002/wcms.27

Abstract Full article on Wiley Online Library:   HTML | PDF
Discrete molecular dynamics

Overview
Elizabeth A. Proctor, Feng Ding, Nikolay V. Dokholyan
Published Online: Jan 21 2011
DOI:10.1002/wcms.4

Abstract Full article on Wiley Online Library:   HTML | PDF
Noncovalent interactions in biochemistry

Overview
Kevin E. Riley, Pavel Hobza
Published Online: Jan 21 2011
DOI:10.1002/wcms.8

Abstract Full article on Wiley Online Library:   HTML | PDF
                                        View Less

Access to this WIREs title is by subscription only.

Recommend to Your
Librarian Now!

The latest WIREs articles in your inbox

Sign Up for Article Alerts