Published in J Comput Chem on July 15, 2003
Chemical screens against a reconstituted multiprotein complex: myricetin blocks DnaJ regulation of DnaK through an allosteric mechanism. Chem Biol (2011) 1.89
AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine. J Mol Model (2005) 1.69
Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comput Biol (2009) 1.67
Allosteric drugs: the interaction of antitumor compound MKT-077 with human Hsp70 chaperones. J Mol Biol (2011) 1.49
Briefly bound to activate: transient binding of a second catalytic magnesium activates the structure and dynamics of CDK2 kinase for catalysis. Structure (2011) 1.21
Novel allosteric sites on Ras for lead generation. PLoS One (2011) 1.20
Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II. J Am Chem Soc (2012) 1.20
Phosphate release coupled to rotary motion of F1-ATPase. Proc Natl Acad Sci U S A (2013) 1.18
RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription. Proc Natl Acad Sci U S A (2010) 1.17
Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations. Proc Natl Acad Sci U S A (2012) 1.14
Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study. Protein Sci (2005) 1.09
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. J Chem Theory Comput (2014) 1.08
The distinct conformational dynamics of K-Ras and H-Ras A59G. PLoS Comput Biol (2010) 1.06
Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. Biochim Biophys Acta (2010) 1.06
How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study. Protein Sci (2006) 1.04
Regulation of RAS oncogenicity by acetylation. Proc Natl Acad Sci U S A (2012) 1.02
Substrate induced population shifts and stochastic gating in the PBCV-1 mRNA capping enzyme. J Am Chem Soc (2009) 1.00
Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase. J Am Chem Soc (2012) 0.99
Dynamic architecture of a protein kinase. Proc Natl Acad Sci U S A (2014) 0.94
Genetically encoded optochemical probes for simultaneous fluorescence reporting and light activation of protein function with two-photon excitation. J Am Chem Soc (2014) 0.91
The structural basis of ATP as an allosteric modulator. PLoS Comput Biol (2014) 0.90
Re-purposing clinical kinase inhibitors to enhance chemosensitivity by overriding checkpoints. Cell Cycle (2014) 0.90
A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase. PLoS Comput Biol (2013) 0.90
Disruption of ionic interactions between the nucleotide binding domain 1 (NBD1) and middle (M) domain in Hsp100 disaggregase unleashes toxic hyperactivity and partial independence from Hsp70. J Biol Chem (2012) 0.90
EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome. Nat Struct Mol Biol (2016) 0.88
How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM study. J Am Chem Soc (2009) 0.87
Kinesin-5 allosteric inhibitors uncouple the dynamics of nucleotide, microtubule, and neck-linker binding sites. Biophys J (2014) 0.86
Two TPX2-dependent switches control the activity of Aurora A. PLoS One (2011) 0.86
Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase. Biochemistry (2010) 0.85
Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2. J Chem Inf Model (2012) 0.85
Dynamic mechanisms for pre-miRNA binding and export by Exportin-5. RNA (2011) 0.84
Loop-loop interactions regulate KaiA-stimulated KaiC phosphorylation in the cyanobacterial KaiABC circadian clock. Biochemistry (2013) 0.84
Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations. PLoS Comput Biol (2011) 0.84
Dynamical allosterism in the mechanism of action of DNA mismatch repair protein MutS. Biophys J (2011) 0.83
The role of conserved water molecules in the catalytic domain of protein kinases. Proteins (2009) 0.83
Relation between the conformational heterogeneity and reaction cycle of Ras: molecular simulation of Ras. Biophys J (2010) 0.82
Revelation of a catalytic calcium-binding site elucidates unusual metal dependence of a human apyrase. J Am Chem Soc (2012) 0.82
Toward understanding the conformational dynamics of RNA ligation. Biochemistry (2009) 0.81
A combined theoretical and experimental study of the ammonia tunnel in carbamoyl phosphate synthetase. J Am Chem Soc (2009) 0.81
Nucleotide binding switches the information flow in ras GTPases. PLoS Comput Biol (2011) 0.81
Quantum mechanics/molecular mechanics investigation of the mechanism of phosphate transfer in human uridine-cytidine kinase 2. Org Biomol Chem (2009) 0.80
Structural and mechanistic insight into covalent substrate binding by Escherichia coli dihydroxyacetone kinase. Proc Natl Acad Sci U S A (2011) 0.80
Binding sensitivity of adefovir to the polymerase from different genotypes of HBV: molecular modeling, docking and dynamics simulation studies. Acta Pharmacol Sin (2012) 0.80
Carbamate transport in carbamoyl phosphate synthetase: a theoretical and experimental investigation. J Am Chem Soc (2010) 0.79
Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins. J Biol Chem (2015) 0.79
Phosphorylation and ATP-binding induced conformational changes in the PrkC, Ser/Thr kinase from B. subtilis. J Comput Aided Mol Des (2010) 0.79
Spectroscopic studies of the Salmonella enterica adenosyltransferase enzyme SeCobA: molecular-level insight into the mechanism of substrate Cob(II)alamin activation. Biochemistry (2014) 0.79
The feasibility of coherent energy transfer in microtubules. J R Soc Interface (2014) 0.79
Recurrent rhinovirus infections in a child with inherited MDA5 deficiency. J Exp Med (2017) 0.78
Analysis of the strength of interfacial hydrogen bonds between tubulin dimers using quantum theory of atoms in molecules. Biophys J (2014) 0.78
Insights into the phosphoryl transfer mechanism of cyclin-dependent protein kinases from ab initio QM/MM free-energy studies. J Phys Chem B (2011) 0.78
ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations. Nucleic Acids Res (2015) 0.78
The state of the guanosine nucleotide allosterically affects the interfaces of tubulin in protofilament. J Comput Aided Mol Des (2012) 0.78
Structural model of weak binding actomyosin in the prepowerstroke state. J Biol Chem (2014) 0.78
A ribokinase family conserved monovalent cation binding site enhances the MgATP-induced inhibition in E. coli phosphofructokinase-2. Biophys J (2013) 0.78
Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution. Nucleic Acids Res (2016) 0.78
Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly. PLoS Comput Biol (2015) 0.77
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors. J Comput Aided Mol Des (2006) 0.77
Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes. PLoS Comput Biol (2015) 0.77
A conserved histidine in switch-II of EF-G moderates release of inorganic phosphate. Sci Rep (2015) 0.77
Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies. PLoS Comput Biol (2016) 0.77
Investigations of the CLOCK and BMAL1 Proteins Binding to DNA: A Molecular Dynamics Simulation Study. PLoS One (2016) 0.77
Exploring the role of the active site cysteine in human muscle creatine kinase. Biochemistry (2006) 0.77
Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases. PLoS Comput Biol (2013) 0.77
SRPK1 and Akt Protein Kinases Phosphorylate the RS Domain of Lamin B Receptor with Distinct Specificity: A Combined Biochemical and In Silico Approach. PLoS One (2016) 0.77
Mechanistic insights into protonation state as a critical factor in hFPPS enzyme inhibition. J Comput Aided Mol Des (2015) 0.76
Determining the Functions of HIV-1 Tat and a Second Magnesium Ion in the CDK9/Cyclin T1 Complex: A Molecular Dynamics Simulation Study. PLoS One (2015) 0.76
A critical residue selectively recruits nucleotides for t7 RNA polymerase transcription fidelity control. Biophys J (2014) 0.76
Identification of key hinge residues important for nucleotide-dependent allostery in E. coli Hsp70/DnaK. PLoS Comput Biol (2013) 0.76
Release of Entropic Spring Reveals Conformational Coupling Mechanism in the ABC Transporter BtuCD-F. Biophys J (2016) 0.76
Molecular determinants of snurportin 1 ligand affinity and structural response upon binding. Biophys J (2009) 0.76
Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case. Biophys J (2015) 0.76
Magnesium-induced nucleophile activation in the guanylyltransferase mRNA capping enzyme. Biochemistry (2012) 0.76
Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana. PLoS One (2016) 0.75
Statistical Thermodynamics for Actin-Myosin Binding: The Crucial Importance of Hydration Effects. Biophys J (2016) 0.75
Oxygen diffusion pathways in a cofactor-independent dioxygenase. Chem Sci (2015) 0.75
Elucidation of the ATP7B N-domain Mg2+-ATP coordination site and its allosteric regulation. PLoS One (2011) 0.75
Evolutionary Covariance Combined with Molecular Dynamics Predicts a Framework for Allostery in the MutS DNA Mismatch Repair Protein. J Phys Chem B (2017) 0.75
Multi-scale computational enzymology: enhancing our understanding of enzymatic catalysis. Int J Mol Sci (2013) 0.75
Adenylylation of Tyr77 stabilizes Rab1b GTPase in an active state: A molecular dynamics simulation analysis. Sci Rep (2016) 0.75
G-actin guides p53 nuclear transport: potential contribution of monomeric actin in altered localization of mutant p53. Sci Rep (2016) 0.75
Mechanism of NTP Binding to the Active Site of T7 RNA Polymerase Revealed by Free-Energy Simulation. Biophys J (2017) 0.75
Designing and Testing of Novel Taxanes to Probe the Highly Complex Mechanisms by Which Taxanes Bind to Microtubules and Cause Cytotoxicity to Cancer Cells. PLoS One (2015) 0.75
ATP and its N⁶-substituted analogues: parameterization, molecular dynamics simulation and conformational analysis. J Mol Model (2010) 0.75
Effects of FGFR2 kinase activation loop dynamics on catalytic activity. PLoS Comput Biol (2017) 0.75
A Novel HRAS Mutation Independently Contributes to Left Ventricular Hypertrophy in a Family with a Known MYH7 Mutation. PLoS One (2016) 0.75
Regulation of signaling directionality revealed by 3D snapshots of a kinase:regulator complex in action. Elife (2016) 0.75
Computer modelling reveals new conformers of the ATP binding loop of Na(+)/K(+)-ATPase involved in the transphosphorylation process of the sodium pump. PeerJ (2017) 0.75
A water-mediated allosteric network governs activation of Aurora kinase A. Nat Chem Biol (2017) 0.75
Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase. Biophys J (2015) 0.75
Mechanistic insights from resolving ligand-dependent kinetics of conformational changes at ATP-gated P2X1R ion channels. Sci Rep (2016) 0.75
Exploring the inhibition mechanism of adenylyl cyclase type 5 by n-terminal myristoylated Gαi1. PLoS Comput Biol (2017) 0.75
Insights into the high fidelity of a DNA polymerase I mutant. J Mol Model (2009) 0.75
Navigating the conformational landscape of G protein-coupled receptor kinases during allosteric activation. J Biol Chem (2017) 0.75
New insights into human farnesyl pyrophosphate synthase inhibition by second-generation bisphosphonate drugs. J Comput Aided Mol Des (2017) 0.75
Oxidative species-induced excitonic transport in tubulin aromatic networks: Potential implications for neurodegenerative disease. J Photochem Photobiol B (2017) 0.75
Binding selectivity of RecA to a single stranded DNA, a computational approach. J Mol Model (2010) 0.75
On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase. Sci Rep (2017) 0.75
Fosfomycin induced structural change in fosfomycin resistance kinases FomA: molecular dynamics and molecular docking studies. J Mol Model (2014) 0.75
Binding MOAD (Mother Of All Databases). Proteins (2005) 2.40
Binding MOAD, a high-quality protein-ligand database. Nucleic Acids Res (2007) 1.99
Chemical screens against a reconstituted multiprotein complex: myricetin blocks DnaJ regulation of DnaK through an allosteric mechanism. Chem Biol (2011) 1.89
CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. J Chem Inf Model (2011) 1.61
Exploring experimental sources of multiple protein conformations in structure-based drug design. J Am Chem Soc (2007) 1.52
Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures. Biophys J (2006) 1.45
CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions. J Chem Inf Model (2011) 1.42
Binding of a small molecule at a protein-protein interface regulates the chaperone activity of hsp70-hsp40. ACS Chem Biol (2010) 1.28
Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models. J Am Chem Soc (2007) 1.28
Full protein flexibility is essential for proper hot-spot mapping. J Am Chem Soc (2010) 1.17
CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series. J Chem Inf Model (2013) 1.17
Solvation influences flap collapse in HIV-1 protease. Proteins (2005) 1.16
Mutagenesis reveals the complex relationships between ATPase rate and the chaperone activities of Escherichia coli heat shock protein 70 (Hsp70/DnaK). J Biol Chem (2010) 1.15
Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case. J Am Chem Soc (2004) 1.15
Computational studies and peptidomimetic design for the human p53-MDM2 complex. Proteins (2005) 1.10
A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket. Biopolymers (2008) 1.10
Protein flexibility and species specificity in structure-based drug discovery: dihydrofolate reductase as a test system. J Am Chem Soc (2007) 1.09
CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. J Chem Inf Model (2013) 1.02
Exploring protein-ligand recognition with Binding MOAD. J Mol Graph Model (2005) 1.00
Incorporating dynamics in E. coli dihydrofolate reductase enhances structure-based drug discovery. J Chem Inf Model (2007) 0.98
Refining the multiple protein structure pharmacophore method: consistency across three independent HIV-1 protease models. J Med Chem (2006) 0.97
Protein flexibility in docking and surface mapping. Q Rev Biophys (2012) 0.96
Novel deletion of lysine 7 expands the clinical, histopathological and genetic spectrum of TPM2-related myopathies. Brain (2013) 0.93
Exploring the composition of protein-ligand binding sites on a large scale. PLoS Comput Biol (2013) 0.90
Improving protocols for protein mapping through proper comparison to crystallography data. J Chem Inf Model (2013) 0.86
Clarifying allosteric control of flap conformations in the 1TW7 crystal structure of HIV-1 protease. Proteins (2009) 0.85
Conformational behavior of beta-proline oligomers. J Am Chem Soc (2003) 0.83
An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases. J Med Chem (2014) 0.82
Chemical probes that selectively recognize the earliest Aβ oligomers in complex mixtures. J Am Chem Soc (2010) 0.82
Computational methods for predicting sites of functionally important dynamics. J Phys Chem B (2009) 0.82
Secondary structural preferences of 2,2-disubstituted pyrrolidine-4-carboxylic acid oligomers: beta-peptide foldamers that cannot form internal hydrogen bonds. J Am Chem Soc (2003) 0.81
The role of tyrosine 71 in modulating the flap conformations of BACE1. Proteins (2011) 0.81
Computational methods for identifying a layered allosteric regulatory mechanism for ALS-causing mutations of Cu-Zn superoxide dismutase 1. Proteins (2011) 0.81
The role of aspartic acid 143 in E. coli tRNA-guanine transglycosylase: insights from mutagenesis studies and computational modeling. Biophys J (2005) 0.80
Parameter choice matters: validating probe parameters for use in mixed-solvent simulations. J Chem Inf Model (2014) 0.80
Biophysical limits of protein-ligand binding. J Chem Inf Model (2012) 0.79
Docking studies and ligand recognition in folylpolyglutamate synthetase. J Med Chem (2005) 0.79
Binding to the open conformation of HIV-1 protease. Proteins (2011) 0.79
A call to arms: what you can do for computational drug discovery. J Chem Inf Model (2011) 0.78
Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design. J Comput Aided Mol Des (2008) 0.78
Quantum mechanical models of the resting state of the vanadium-dependent haloperoxidase. Inorg Chem (2004) 0.77
Identification of key hinge residues important for nucleotide-dependent allostery in E. coli Hsp70/DnaK. PLoS Comput Biol (2013) 0.76
Overcoming sequence misalignments with weighted structural superposition. Proteins (2012) 0.75
The 12-minute journey. Narrat Inq Bioeth (2014) 0.75