Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow.
PLoS Comput. Biol., 2022
Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation.
J. Chem. Inf. Model., 2022
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization.
J. Chem. Inf. Model., 2021
Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets.
BMC Bioinform., 2021
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python.
Bioinform., 2021
ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution.
Bioinform., 2021
Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel.
PLoS Comput. Biol., 2020
Rhapsody: predicting the pathogenicity of human missense variants.
Bioinform., 2020
QuartataWeb: Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics.
Bioinform., 2020
Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members.
J. Chem. Inf. Model., 2019
DynOmics: dynamics of structural proteome and beyond.
Nucleic Acids Res., 2017
<i>i</i>GNM 2.0: the Gaussian network model database for biomolecular structural dynamics.
Nucleic Acids Res., 2016
The center for causal discovery of biomedical knowledge from big data.
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J. Am. Medical Informatics Assoc., 2015
Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution.
Bioinform., 2015
The anisotropic network model web server at 2015 (ANM 2.0).
Bioinform., 2015
BalestraWeb: efficient online evaluation of drug-target interactions.
Bioinform., 2015
ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones.
PLoS Comput. Biol., 2014
Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model.
PLoS Comput. Biol., 2014
Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle.
PLoS Comput. Biol., 2014
<i>Evol</i> and <i>ProDy</i> for bridging protein sequence evolution and structural dynamics.
Bioinform., 2014
Predicting Drug-Target Interactions Using Probabilistic Matrix Factorization.
J. Chem. Inf. Model., 2013
Coupling between Catalytic Loop Motions and Enzyme Global Dynamics.
PLoS Comput. Biol., 2012
Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members.
PLoS Comput. Biol., 2011
<i>ProDy</i>: Protein Dynamics Inferred from Theory and Experiments.
Bioinform., 2011
Computational Generation inhibitor-Bound Conformers of P38 Map Kinase and Comparison with Experiments.
Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011
On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm.
PLoS Comput. Biol., 2010
Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs.
PLoS Comput. Biol., 2010
Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology.
PLoS Comput. Biol., 2010
Toward Understanding Allosteric Signaling Mechanisms in the ATPase Domain of Molecular Chaperones.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010
Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL.
PLoS Comput. Biol., 2009
Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models.
PLoS Comput. Biol., 2009
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics.
Bioinform., 2009
Analysis of correlated mutations in HIV-1 protease using spectral clustering.
Bioinform., 2008
Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations.
PLoS Comput. Biol., 2007
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations.
PLoS Comput. Biol., 2007
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics.
J. Comput. Biol., 2007
Recruitment of rare <i>3</i>-grams at functional sites: Is this a mechanism for increasing enzyme specificity?
BMC Bioinform., 2007
Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices.
Bioinform., 2007
Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007
<i>o</i>GNM: online computation of structural dynamics using the Gaussian Network Model.
Nucleic Acids Res., 2006
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, <i>Saccharomyces cerevisiae</i>.
BMC Bioinform., 2006
Anisotropic network model: systematic evaluation and a new web interface.
Bioinform., 2006
<i>i</i>GNM: a database of protein functional motions based on Gaussian Network Model.
Bioinform., 2005
Mining frequent patterns in protein structures: a study of protease families.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004
Protein Functional Motion Query and Visualization.
Proceedings of the 28th International Computer Software and Applications Conference (COMPSAC 2004), 2004
Dynamics of large proteins through hierarchical levels of coarse-grained structures.
J. Comput. Chem., 2002