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
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WIREs Comput Mol Sci
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Computational Biochemistry and Biophysics
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Computational Biochemistry and Biophysics
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
Machine learning, artificial intelligence, and data science breaking into drug design and neglected diseases
Advanced Review
José Peña‐Guerrero, Paul A. Nguewa, Alfonso T. García‐Sosa
Published Online: Jan 05 2021
DOI:10.1002/wcms.1513
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
Establishing the allosteric mechanism in CRISPR‐Cas9
Advanced Review
Łukasz Nierzwicki, Pablo Ricardo Arantes, Aakash Saha, Giulia Palermo
Published Online: Oct 27 2020
DOI:10.1002/wcms.1503
Computational aspects towards understanding the photoprocesses in eumelanin
Focus Article
Debashree Ghosh
Published Online: Oct 12 2020
DOI:10.1002/wcms.1505
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
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
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
The prospects of quantum computing in computational molecular biology
Advanced Review
Carlos Outeiral, Martin Strahm, Jiye Shi, Garrett M. Morris, Simon C. Benjamin, Charlotte M. Deane
Published Online: May 22 2020
DOI:10.1002/wcms.1481
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
In silico toxicology: From structure–activity relationships towards deep learning and adverse outcome pathways
Advanced Review
Jennifer Hemmerich, Gerhard F. Ecker
Published Online: Mar 31 2020
DOI:10.1002/wcms.1475
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
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
Ligand binding free energy and kinetics calculation in 2020
Advanced Review
Vittorio Limongelli
Published Online: Jan 09 2020
DOI:10.1002/wcms.1455
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
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
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
Learning from nature: Understanding hydrogenase enzyme using computational approach
Advanced Review
Chenghua Sun, Shaohua Shen, Yongjun Xu, Qinye Li, Siyao Qiu
Published Online: May 28 2019
DOI:10.1002/wcms.1422
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
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
Molecular dynamics simulations of macromolecular crystals
Advanced Review
David S. Cerutti, David A. Case
Published Online: Nov 16 2018
DOI:10.1002/wcms.1402
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
Electronic energy transfer in biomacromolecules
Advanced Review
Carles Curutchet, Benedetta Mennucci, Marina Corbella, Lorenzo Cupellini
Published Online: Sep 13 2018
DOI:10.1002/wcms.1392