Department of Computational Medicine and Bioinformatics
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LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis.
Biophysical journal Jul, 2012 | Pubmed ID: 22828348
Domain-opening and dynamic coupling in the α-subunit of heterotrimeric G proteins.
Biophysical journal Jul, 2013 | Pubmed ID: 23870276
sgTarget: a target selection resource for structural genomics.
Nucleic acids research Jul, 2006 | Pubmed ID: 16844998
Bio3d: an R package for the comparative analysis of protein structures.
Bioinformatics (Oxford, England) Nov, 2006 | Pubmed ID: 16940322
Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain.
Journal of molecular biology May, 2007 | Pubmed ID: 17399740
The 2006 automated function prediction meeting.
BMC bioinformatics May, 2007 | Pubmed ID: 17570143
Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins.
Structure (London, England : 1993) Jun, 2008 | Pubmed ID: 18547521
Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.
PLoS computational biology Mar, 2009 | Pubmed ID: 19300489
Large conformational changes in proteins: signaling and other functions.
Current opinion in structural biology Apr, 2010 | Pubmed ID: 20060708
The distinct conformational dynamics of K-Ras and H-Ras A59G.
PLoS computational biology , 2010 | Pubmed ID: 20838576
Conformational selection in G-proteins: lessons from Ras and Rho.
Biophysical journal Dec, 2010 | Pubmed ID: 21112273
Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics.
PLoS computational biology Apr, 2011 | Pubmed ID: 21533070
Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation.
PLoS computational biology Oct, 2011 | Pubmed ID: 22022240
Novel allosteric sites on Ras for lead generation.
PloS one , 2011 | Pubmed ID: 22046245
Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein.
Biochemistry Dec, 2011 | Pubmed ID: 22050600
Electrostatically biased binding of kinesin to microtubules.
PLoS biology Nov, 2011 | Pubmed ID: 22140358
Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire.
Proceedings of the National Academy of Sciences of the United States of America Jun, 2012 | Pubmed ID: 22645359
Identification of potential small molecule binding pockets on Rho family GTPases.
PloS one , 2012 | Pubmed ID: 22815826
Calcium binding and allosteric signaling mechanisms for the sarcoplasmic reticulum Ca²+ ATPase.
Protein science : a publication of the Protein Society Oct, 2012 | Pubmed ID: 22821874
Mapping the structural and dynamical features of kinesin motor domains.
PLoS computational biology , 2013 | Pubmed ID: 24244137
Novel procedure for thermal equilibration in molecular dynamics simulation.
Molecular simulation Apr, 2009 | Pubmed ID: 25125797
Kinesin-5 allosteric inhibitors uncouple the dynamics of nucleotide, microtubule, and neck-linker binding sites.
Biophysical journal Nov, 2014 | Pubmed ID: 25418105
Integrating protein structural dynamics and evolutionary analysis with Bio3D.
BMC bioinformatics Dec, 2014 | Pubmed ID: 25491031
Enrichment of druggable conformations from apo protein structures using cosolvent-accelerated molecular dynamics.
Biology Apr, 2015 | Pubmed ID: 25906084
Mapping the Processivity Determinants of the Kinesin-3 Motor Domain.
Biophysical journal Oct, 2015 | Pubmed ID: 26488644
Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins.
The Journal of biological chemistry Feb, 2016 | Pubmed ID: 26703464
Rapid Characterization of Allosteric Networks with Ensemble Normal Mode Analysis.
The journal of physical chemistry. B Aug, 2016 | Pubmed ID: 27056373
Online interactive analysis of protein structure ensembles with Bio3D-web.
Bioinformatics (Oxford, England) Nov, 2016 | Pubmed ID: 27423893
Systems Structural Biology Analysis of Ligand Effects on ERα Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.
Cell chemical biology Jan, 2017 | Pubmed ID: 28042045
Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers.
Scientific reports Jan, 2017 | Pubmed ID: 28067274
Structural and Molecular Mechanisms of Cytokine-Mediated Endocrine Resistance in Human Breast Cancer Cells.
Molecular cell Mar, 2017 | Pubmed ID: 28306507
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