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WIREs Comput Mol Sci
Impact Factor: 16.778

Computational Biochemistry and Biophysics

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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

Abstract Full article on Wiley Online Library:   HTML | PDF
NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient

Advanced Review
Rubén Laplaza, Francesca Peccati, Roberto A. Boto, Chaoyu Quan, Alessandra Carbone, Jean‐Philip Piquemal, Yvon Maday, Julia Contreras‐García
Published Online: Aug 24 2020
DOI:10.1002/wcms.1497

Abstract Full article on Wiley Online Library:   HTML | PDF
TeraChem: A graphical processing unit‐accelerated electronic structure package for large‐scale ab initio molecular dynamics

Software Focus
Stefan Seritan, Christoph Bannwarth, Bryan S. Fales, Edward G. Hohenstein, Christine M. Isborn, Sara I. L. Kokkila‐Schumacher, Xin Li, Fang Liu, Nathan Luehr, James W. Snyder, Chenchen Song, Alexey V. Titov, Ivan S. Ufimtsev, Lee‐Ping Wang, Todd J. Martínez
Published Online: Jul 26 2020
DOI:10.1002/wcms.1494

Abstract Full article on Wiley Online Library:   HTML | PDF
The prospects of quantum computing in computational molecular biology

Advanced Review
Charlotte M. Deane, Simon C. Benjamin, Garrett M. Morris, Jiye Shi, Martin Strahm, Carlos Outeiral
Published Online: May 23 2020
DOI:10.1002/wcms.1481

Abstract Full article on Wiley Online Library:   HTML | PDF
Structural prediction of protein interactions and docking using conservation and coevolution

Advanced Review
Raphael Guerois, Chloé Quignot, Jessica Andreani
Published Online: May 02 2020
DOI:10.1002/wcms.1470

Abstract Full article on Wiley Online Library:   HTML | PDF
In silico toxicology: From structure–activity relationships towards deep learning and adverse outcome pathways

Advanced Review
Gerhard F. Ecker, Jennifer Hemmerich
Published Online: Mar 31 2020
DOI:10.1002/wcms.1475

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational studies of DNA repair: Insights into the function of monofunctional DNA glycosylases in the base excision repair pathway

Focus Article
Rajwinder Kaur, Dylan J. Nikkel, Stacey D. Wetmore
Published Online: Mar 15 2020
DOI:10.1002/wcms.1471

Abstract Full article on Wiley Online Library:   HTML | PDF
P2Y1‐like nucleotide receptors—Structures, molecular modeling, mutagenesis, and oligomerization

Overview
Alexander Neumann, Christa E. Müller, Vigneshwaran Namasivayam
Published Online: Mar 03 2020
DOI:10.1002/wcms.1464

Abstract Full article on Wiley Online Library:   HTML | PDF
Ligand binding free energy and kinetics calculation in 2020

Advanced Review
Vittorio Limongelli
Published Online: Jan 09 2020
DOI:10.1002/wcms.1455

Abstract Full article on Wiley Online Library:   HTML | PDF
Interrogating chemical mechanisms in natural products biosynthesis using quantum chemical calculations

Advanced Review
Dean J. Tantillo
Published Online: Nov 20 2019
DOI:10.1002/wcms.1453

Abstract Full article on Wiley Online Library:   HTML | PDF
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

Abstract Full article on Wiley Online Library:   HTML | PDF
Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling

Advanced Review
Stephanie Portillo‐Ledesma, Tamar Schlick
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 A. Case, David S. Cerutti
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
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

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
Daniel‐Adriano Silva, Enrique Marcos
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
Charleen G. Don, Martin Smieško
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
Jelisa Iglesias, Suwipa Saen‐oon, Robert Soliva, Victor Guallar
Published Online: Apr 29 2018
DOI:10.1002/wcms.1367

Abstract Full article on Wiley Online Library:   HTML | PDF
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