Published in Annu Rev Biophys on January 01, 2010
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A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein. PLoS Comput Biol (2013) 0.88
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Predicting protein flexibility through the prediction of local structures. Proteins (2010) 0.87
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Experiments on Hemoglobin in Single Crystals and Silica Gels Distinguish among Allosteric Models. Biophys J (2015) 0.86
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Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications. PLoS Comput Biol (2014) 0.85
Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics. PLoS One (2012) 0.85
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Dynamical basis for drug resistance of HIV-1 protease. BMC Struct Biol (2011) 0.85
Exploration of multi-state conformational dynamics and underlying global functional landscape of maltose binding protein. PLoS Comput Biol (2012) 0.84
Utilizing experimental data for reducing ensemble size in flexible-protein docking. J Chem Inf Model (2011) 0.84
Characterizing protein motions from structure. J Mol Graph Model (2011) 0.84
Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery. PLoS Comput Biol (2016) 0.84
Endoglucanases: insights into thermostability for biofuel applications. Biotechnol Biofuels (2013) 0.83
Interconversion of functional motions between mesophilic and thermophilic adenylate kinases. PLoS Comput Biol (2011) 0.83
Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion. Proteins (2011) 0.83
Cooperative Dynamics of Intact AMPA and NMDA Glutamate Receptors: Similarities and Subfamily-Specific Differences. Structure (2015) 0.83
Flexibility within the rotor and stators of the vacuolar H+-ATPase. PLoS One (2013) 0.83
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The dynamic AMPA receptor extracellular region: a platform for synaptic protein interactions. J Physiol (2016) 0.82
Large-scale motions in the adenylate kinase solution ensemble: coarse-grained simulations and comparison with solution X-ray scattering. Chem Phys (2012) 0.82
Adaptability of protein structures to enable functional interactions and evolutionary implications. Curr Opin Struct Biol (2015) 0.82
"Fluctuograms" reveal the intermittent intra-protein communication in subtilisin Carlsberg and correlate mechanical coupling with co-evolution. PLoS Comput Biol (2011) 0.81
Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics. PLoS Comput Biol (2013) 0.81
Characterization of protein flexibility using small-angle x-ray scattering and amplified collective motion simulations. Biophys J (2014) 0.81
Allosteric inhibition of individual enzyme molecules trapped in lipid vesicles. Proc Natl Acad Sci U S A (2012) 0.81
Differential modulation of functional dynamics and allosteric interactions in the Hsp90-cochaperone complexes with p23 and Aha1: a computational study. PLoS One (2013) 0.81
Measuring and modeling diffuse scattering in protein X-ray crystallography. Proc Natl Acad Sci U S A (2016) 0.81
Conformational variation of an extreme drug resistant mutant of HIV protease. J Mol Graph Model (2015) 0.80
Communication over the network of binary switches regulates the activation of A2A adenosine receptor. PLoS Comput Biol (2015) 0.80
Coarse-Grained Models for Protein-Cell Membrane Interactions. Polymers (Basel) (2015) 0.80
Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association. Proteins (2015) 0.80
Quantification of Drive-Response Relationships Between Residues During Protein Folding. J Chem Theory Comput (2013) 0.80
Substrate recognition and motion mode analyses of PFV integrase in complex with viral DNA via coarse-grained models. PLoS One (2013) 0.80
Elastic network normal modes provide a basis for protein structure refinement. J Chem Phys (2012) 0.80
iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Res (2015) 0.80
Normal modes of prion proteins: from native to infectious particle. Biochemistry (2011) 0.80
Designing allostery-inspired response in mechanical networks. Proc Natl Acad Sci U S A (2017) 0.79
Structure, Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains. Biophys J (2015) 0.79
Identification of motions in membrane proteins by elastic network models and their experimental validation. Methods Mol Biol (2012) 0.79
Protein dynamics governed by interfaces of high polarity and low packing density. PLoS One (2012) 0.79
Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins. BMC Struct Biol (2012) 0.79
Ligand promiscuity through the eyes of the aminoglycoside N3 acetyltransferase IIa. Protein Sci (2013) 0.79
AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems. Entropy (Basel) (2015) 0.78
Distributions of experimental protein structures on coarse-grained free energy landscapes. J Chem Phys (2015) 0.78
Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering. Comput Struct Biotechnol J (2012) 0.78
Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks. PLoS One (2011) 0.78
BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures. J Chem Inf Model (2014) 0.78
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol (2016) 0.78
Allosteric regulation of the Hsp90 dynamics and stability by client recruiter cochaperones: protein structure network modeling. PLoS One (2014) 0.78
A flexible docking scheme efficiently captures the energetics of glycan-cyanovirin binding. Biophys J (2014) 0.78
How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics. Biophys J (2015) 0.78
A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins. Structure (2015) 0.78
Challenges in structural approaches to cell modeling. J Mol Biol (2016) 0.78
Possible origin of life between mica sheets: does life imitate mica? J Biomol Struct Dyn (2012) 0.78
Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication. PLoS Comput Biol (2017) 0.77
Assembly and analysis of eukaryotic Argonaute-RNA complexes in microRNA-target recognition. Nucleic Acids Res (2015) 0.77
Protein dynamics of the HIF-2α PAS-B domain upon heterodimerization and ligand binding. PLoS One (2014) 0.77
Ligand-induced protein responses and mechanical signal propagation described by linear response theories. Biophys J (2014) 0.77
Crystal structure of Onconase at 1.1 Å resolution--insights into substrate binding and collective motion. FEBS J (2011) 0.77
Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution. Evol Appl (2015) 0.77
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