Research graph
References from CHAPERON g : A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/nsb0902-646
10.1038/nsb0902-646 · External reference
10.1016/j.neuron.2018.08.011
10.1016/j.neuron.2018.08.011 · External reference
Molecular dynamics simulations: advances and applications
2015 · External reference
10.1002/jcc.20291
10.1002/jcc.20291 · External reference
Molecular dynamics simulation by GROMACS using GUI plugin for PyMOL
10.1021/ci400071x · 2013 · External reference
YAMACS: a graphical interface for GROMACS
10.1093/bioinformatics/btac573 · 2022 · External reference
MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations
10.1093/bib/bbad057 · 2023 · External reference
Visual dynamics: a web application for molecular dynamics simulation using GROMACS
2023 · External reference
10.1093/nar/gkac380
10.1093/nar/gkac380 · External reference
10.1016/j.compbiolchem.2020.107322
10.1016/j.compbiolchem.2020.107322 · External reference
MD DaVis:: interactive data visualization of protein molecular dynamics
10.1093/bioinformatics/btac314 · 2022 · External reference
GUIMACS-a Java based front end for GROMACS
10.3233/isb-00278 · 2007 · External reference
10.1021/ci900248f
10.1021/ci900248f · External reference
Gromita: a fully integrated graphical user interface to gromacs 4
10.4137/bbi.s3207 · 2009 · External reference
Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of pca analysis
10.1007/s00894-016-2982-4 · 2016 · External reference
Enlighten2: molecular dynamics simulations of protein-ligand systems made accessible
10.1093/bioinformatics/btaa643 · 2020 · External reference
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations
10.1093/bioinformatics/bts139 · 2012 · External reference
Unresolved reference
External reference
10.1002/jcc.20945
10.1002/jcc.20945 · External reference
10.1038/s41586-020-2649-2
10.1038/s41586-020-2649-2 · External reference
10.1038/s41592-019-0686-2
10.1038/s41592-019-0686-2 · External reference
10.1109/mcse.2007.55
10.1109/mcse.2007.55 · External reference
Unresolved reference
External reference
10.1002/bip.360221211
10.1002/bip.360221211 · External reference
From proteins to perturbed Hamiltonians: a suite of tutorials for the GROMACS-2018 molecular simulation package [article v1.0]
10.33011/livecoms.1.1.5068 · 2018 · External reference
Identifying potential p53-MDM2 interaction antagonists: an integrated approach of pharmacophore-based virtual screening, interaction fingerprinting, MD simulation and DFT studies
10.1002/slct.202202380 · 2022 · External reference
10.1021/jp9110794
10.1021/jp9110794 · External reference
Revealing the favorable dissociation pathway of type ii kinase inhibitors via enhanced sampling simulations and two-end-state calculations
10.1038/srep08457 · 2015 · External reference
10.1002/jcc.540130812
10.1002/jcc.540130812 · External reference
10.1016/s0010-4655(00)00215-0
10.1016/s0010-4655(00)00215-0 · External reference
10.1002/jcc.21367
10.1002/jcc.21367 · External reference
ACPYPE–antechamber python parser interface
10.1186/1756-0500-5-367 · 2012 · External reference
PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules
10.1007/bf00355047 · 1996 · External reference
10.1093/nar/gkx312
10.1093/nar/gkx312 · External reference
Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase Geobacillus zalihae revealed a better structure
10.3390/molecules22101574 · 2017 · External reference
Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis
10.1371/journal.pone.0119264 · 2015 · External reference
How molecular size impacts RMSD applications in molecular dynamics simulations
10.1021/acs.jctc.7b00028 · 2017 · External reference
10.1080/07391102.2020.1792346
10.1080/07391102.2020.1792346 · External reference
Radius of gyration as an indicator of protein structure compactness
10.1134/s0026893308040195 · 2008 · External reference
Solvent accessibility of residues undergoing pathogenic variations in humans: from protein structures to protein sequences
10.3389/fmolb.2020.626363 · 2021 · External reference
10.1002/jcc.540160303
10.1002/jcc.540160303 · External reference
10.1016/0022-2836(73)90011-9
10.1016/0022-2836(73)90011-9 · External reference
Unresolved reference
2014 · External reference
Validating clustering of molecular dynamics simulations using polymer models
10.1186/1471-2105-12-445 · 2011 · External reference
Unresolved reference
2015 · External reference
Protein dynamics, thermal stability, and free-energy landscapes: a molecular dynamics investigation
10.1016/s0006-3495(03)74687-6 · 2003 · External reference
10.1016/j.jmgm.2009.01.006
10.1016/j.jmgm.2009.01.006 · External reference
10.1021/ci500020m
10.1021/ci500020m · External reference
Unresolved reference
External reference
10.1021/acs.jctc.8b00391
10.1021/acs.jctc.8b00391 · External reference
An in silico approach to determine inter-subunit affinities in human septin complexes
2023 · External reference
Effective estimation of ligand-binding affinity using biased sampling method
10.1021/acsomega.8b03258 · 2019 · External reference
Unbinding ligands from SARS-CoV-2 Mpro via umbrella sampling simulations
10.1098/rsos.211480 · 2022 · External reference
Csc01 shows promise as a potential inhibitor of the oncogenic G13D mutant of KRAS: an in silico approach
2023 · External reference
Delineation of the CENP-LN sub-complex dissociation mechanism upon multisite phosphorylation during mitosis
2023 · External reference
