Research graph
References from Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1093/bioinformatics/btm378
10.1093/bioinformatics/btm378 · External reference
10.1002/jcc.21688
10.1002/jcc.21688 · External reference
10.1002/jcc.21287
10.1002/jcc.21287 · External reference
Charmm - a program for macromolecular energy, minimization, and dynamics calculations
10.1002/jcc.540040211 · 1983 · External reference
JGromacs: a Java package for analyzing protein simulations
10.1021/ci200289s · 2012 · External reference
10.1093/bioinformatics/btt055
10.1093/bioinformatics/btt055 · External reference
10.1002/jcc.20290
10.1002/jcc.20290 · External reference
10.1016/0263-7855(96)00018-5
10.1016/0263-7855(96)00018-5 · External reference
Unresolved reference
External reference
10.1016/j.jmgm.2003.12.005
10.1016/j.jmgm.2003.12.005 · External reference
Software news and updates carma: a molecular dynamics analysis program
10.1002/jcc.20482 · 2006 · External reference
Essential dynamics: a tool for efficient trajectory compression and management
10.1021/ct050285b · 2006 · External reference
10.1093/bioinformatics/btl461
10.1093/bioinformatics/btl461 · External reference
10.1002/pro.3923
10.1002/pro.3923 · External reference
The molecular modeling toolkit: a new approach to molecular simulations
10.1002/(sici)1096-987x(20000130)21:2<79::aid-jcc1>3.0.co;2-b · 2000 · External reference
Biskit—a software platform for structural bioinformatics
10.1093/bioinformatics/btl655 · 2007 · External reference
10.1093/bioinformatics/btu336
10.1093/bioinformatics/btu336 · External reference
MD-TASK: a software suite for analyzing molecular dynamics trajectories
10.1093/bioinformatics/btx349 · 2017 · External reference
10.1016/j.bpj.2015.08.015
10.1016/j.bpj.2015.08.015 · External reference
10.1002/jcc.21787
10.1002/jcc.21787 · External reference
A network representation of protein structures: implications for protein stability
10.1529/biophysj.105.064485 · 2005 · External reference
10.1002/prot.21565
10.1002/prot.21565 · External reference
One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers
10.1021/jp060039b · 2006 · External reference
Measuring and testing dependence by correlation of distances, annals of statistics
10.1214/009053607000000505 · 2007 · External reference
10.1021/ct300206j
10.1021/ct300206j · External reference
10.1006/jmbi.1995.0423
10.1006/jmbi.1995.0423 · External reference
Analysis of multidomain protein dynamics
10.1021/acs.jctc.5b00796 · 2016 · External reference
A practical guide to wavelet analysis
10.1175/1520-0477(1998)079<0061:apgtwa>2.0.co;2 · 1998 · External reference
Wavelet analysis of protein motion
2012 · External reference
10.1371/journal.pcbi.1000480
10.1371/journal.pcbi.1000480 · External reference
Locating the active sites of enzymes using mechanical properties
10.1002/prot.21353 · 2007 · External reference
10.1007/s12038-007-0089-x
10.1007/s12038-007-0089-x · External reference
10.1371/journal.pcbi.1002749
10.1371/journal.pcbi.1002749 · External reference
10.1371/journal.pcbi.1000544
10.1371/journal.pcbi.1000544 · External reference
10.1371/journal.pcbi.1002154
10.1371/journal.pcbi.1002154 · External reference
10.1016/j.str.2015.07.002
10.1016/j.str.2015.07.002 · External reference
Allostery and epistasis: emergent properties of anisotropic networks
2020 · External reference
10.1016/s0006-3495(93)81293-1
10.1016/s0006-3495(93)81293-1 · External reference
10.1016/s0263-7855(97)00009-x
10.1016/s0263-7855(97)00009-x · External reference
10.1016/j.str.2018.07.019
10.1016/j.str.2018.07.019 · External reference
On the permeation of large organic cations through the pore of ATP-gated P2X receptors
10.1073/pnas.1701379114 · 2017 · External reference
A gating mechanism of pentameric ligand-gated ion channels
10.1073/pnas.1313785110 · 2013 · External reference
Elastic energy storage in beta-sheets with application to F1-ATPase
10.1007/s00249-003-0335-6 · 2004 · External reference
10.1016/j.jcp.2011.01.048
10.1016/j.jcp.2011.01.048 · External reference
Calculating center of mass in an unbounded 2D environment
2011 · External reference
A new algorithm for exhaustive ring perception in a molecular graph
10.1021/ci960322f · 1996 · External reference
Interpreting correlated motions using normal mode analysis
10.1016/j.str.2006.09.003 · 2006 · External reference
10.1002/prot.20784
10.1002/prot.20784 · External reference
10.1038/366654a0
10.1038/366654a0 · External reference
10.1021/acs.jctc.6b00813
10.1021/acs.jctc.6b00813 · External reference
A graphical aid to the interpretation and validation of cluster analysis
10.1016/0377-0427(87)90125-7 · 1987 · External reference
10.1126/science.1062023
10.1126/science.1062023 · External reference
10.1126/stke.2502004re13
10.1126/stke.2502004re13 · External reference
A database of macromolecular motions
10.1093/nar/26.18.4280 · 1998 · External reference
10.1016/j.jmb.2007.02.049
10.1016/j.jmb.2007.02.049 · External reference
10.1371/journal.pcbi.1006364
10.1371/journal.pcbi.1006364 · External reference
The distinct conformational dynamics of K-Ras and H-Ras A59G
10.1371/journal.pcbi.1000922 · 2010 · External reference
A comparison of multiscale methods for the analysis of molecular dynamics simulations
10.1021/jp302103t · 2012 · External reference
Using wavelet analysis to assist in identification of significant events in molecular dynamics simulations
10.1021/acs.jcim.5b00727 · 2016 · External reference
10.1110/ps.037473.108
10.1110/ps.037473.108 · External reference
Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data
10.1093/protein/gzn015 · 2008 · External reference
Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations
10.1093/protein/gzn012 · 2008 · External reference
10.1016/j.str.2010.01.012
10.1016/j.str.2010.01.012 · External reference
10.1021/acs.jcim.9b00271
10.1021/acs.jcim.9b00271 · External reference
10.1016/j.csbj.2022.09.016 · Admitted local publication
10.1021/acs.jcim.5b00122
10.1021/acs.jcim.5b00122 · External reference
10.1016/j.str.2009.12.015
10.1016/j.str.2009.12.015 · External reference
Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling
10.1038/s41467-019-13227-w · 2019 · External reference
10.1021/acs.chemrev.9b00106
10.1021/acs.chemrev.9b00106 · External reference
A molecular mechanism for transthyretin amyloidogenesis
10.1038/s41467-019-08609-z · 2019 · External reference
Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit
2018 · External reference
Structural insights into dynamics of RecU-HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state
10.1093/nar/gkw1165 · 2017 · External reference
Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape
10.1073/pnas.1604012113 · 2016 · External reference
The gearbox of the bacterial flagellar motor switch
10.1016/j.str.2016.05.012 · 2016 · External reference
10.1073/pnas.1519609113
10.1073/pnas.1519609113 · External reference
Collective dynamics underlying allosteric transitions in hemoglobin
10.1371/journal.pcbi.1003232 · 2013 · External reference
10.1371/journal.pcbi.1001098
10.1371/journal.pcbi.1001098 · External reference
Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases
10.1371/journal.pcbi.1003207 · 2013 · External reference
10.1016/j.bbamem.2020.183355
10.1016/j.bbamem.2020.183355 · External reference
10.1371/journal.pcbi.1003679
10.1371/journal.pcbi.1003679 · External reference
10.1371/journal.pone.0186089
10.1371/journal.pone.0186089 · External reference
10.1371/journal.pcbi.1005299
10.1371/journal.pcbi.1005299 · External reference
10.1021/acs.jcim.1c00766
10.1021/acs.jcim.1c00766 · External reference
10.1021/acs.jctc.1c00372
10.1021/acs.jctc.1c00372 · External reference
Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation
2021 · External reference
Enzyme closure and nucleotide binding structurally lock guanylate kinase
10.1016/j.bpj.2011.07.048 · 2011 · External reference
Functional modes and residue flexibility control the anisotropic response of guanylate kinase to mechanical stress
10.1016/j.bpj.2010.09.026 · 2010 · External reference
10.1021/ja202587a
10.1021/ja202587a · External reference
Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography
10.1038/s41598-017-02097-1 · 2017 · External reference
10.1016/j.jmb.2016.11.005
10.1016/j.jmb.2016.11.005 · External reference
10.1103/physrevlett.94.078102
10.1103/physrevlett.94.078102 · External reference
Manipulation of conformational change in proteins by single-residue perturbations
10.1016/j.bpj.2010.05.020 · 2010 · External reference
Subtle pH differences trigger single residue motions for moderating conformations of calmodulin
10.1063/1.3651807 · 2011 · External reference
10.1371/journal.pcbi.1003624
10.1371/journal.pcbi.1003624 · External reference
10.1016/j.str.2014.11.011
10.1016/j.str.2014.11.011 · External reference
10.1016/j.bpj.2015.06.060
10.1016/j.bpj.2015.06.060 · External reference
10.1021/acs.jcim.6b00775
10.1021/acs.jcim.6b00775 · External reference
10.1038/s41598-017-10571-z
10.1038/s41598-017-10571-z · External reference
Structural dynamics is a determinant of the functional significance of missense variants
10.1073/pnas.1715896115 · 2018 · External reference
10.1021/acs.jcim.7b00630
10.1021/acs.jcim.7b00630 · External reference
Unraveling the motions behind enterovirus 71 uncoating
10.1016/j.bpj.2017.12.021 · 2018 · External reference
Dissecting structure-encoded determinants of allosteric cross-talk between post-translational modification sites in the Hsp90 chaperones
10.1038/s41598-018-25329-4 · 2018 · External reference
10.1021/acs.jcim.9b00006
10.1021/acs.jcim.9b00006 · External reference
10.1021/acs.jctc.9b00119
10.1021/acs.jctc.9b00119 · External reference
Dynamics, nanomechanics and signal transduction in reelin repeats
10.1038/s41598-019-55461-8 · 2019 · External reference
Comparative dynamics and functional mechanisms of the CYP17A1 tunnels regulated by ligand binding
10.1021/acs.jcim.0c00447 · 2020 · External reference
10.1021/acs.jcim.9b01045
10.1021/acs.jcim.9b01045 · External reference
10.1016/j.csbj.2021.07.017 · Admitted local publication
Hinge-shift mechanism as a protein design principle for the evolution of beta-lactamases from substrate promiscuity to specificity
10.1038/s41467-021-22089-0 · 2021 · External reference
Structural and dynamic effects of PTEN C-terminal tail phosphorylation
10.1021/acs.jcim.2c00441 · 2022 · External reference
10.1016/j.bpj.2022.03.012
10.1016/j.bpj.2022.03.012 · External reference
10.1016/j.neuron.2016.03.032
10.1016/j.neuron.2016.03.032 · External reference
10.1016/j.neuropharm.2014.12.006
10.1016/j.neuropharm.2014.12.006 · External reference
Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics
10.1371/journal.pcbi.1005784 · 2017 · External reference
Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel
2021 · External reference
10.1126/sciadv.adc9340
10.1126/sciadv.adc9340 · External reference
10.1016/j.jmb.2014.07.030
10.1016/j.jmb.2014.07.030 · External reference
Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function
10.1016/j.heliyon.2021.e08220 · 2021 · External reference
10.1039/c3sm52345d
10.1039/c3sm52345d · External reference
10.1039/c2cs15302e
10.1039/c2cs15302e · External reference
10.1039/c6cp05249e
10.1039/c6cp05249e · External reference
10.1021/ja107882e
10.1021/ja107882e · External reference
10.1016/j.csbj.2021.12.044
10.1016/j.csbj.2021.12.044 · External reference
webPSN v2.0: a webserver to infer fingerprints of structural communication in biomacromolecules
10.1093/nar/gkaa397 · 2020 · External reference
10.1021/acs.jcim.9b00665
10.1021/acs.jcim.9b00665 · External reference
Surviving the deluge of biosimulation data
2020 · External reference
