Published in Proteins on May 15, 2004
Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput Biol (2007) 1.67
iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinformatics (2005) 1.65
The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models. J Chem Theory Comput (2006) 1.33
Functional dynamics of PDZ binding domains: a normal-mode analysis. Biophys J (2005) 1.11
HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics. Biophys J (2007) 1.05
Wiggle-predicting functionally flexible regions from primary sequence. PLoS Comput Biol (2006) 1.03
Evolutionary conservation of protein backbone flexibility. J Mol Evol (2006) 1.02
Probing the flexibility of large conformational changes in protein structures through local perturbations. PLoS Comput Biol (2009) 1.02
Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits. Biophys J (2009) 0.99
Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families. Protein Sci (2008) 0.99
Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives. Bioinform Biol Insights (2008) 0.99
Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant. Biophys J (2005) 0.93
Analysis of domain movements in glutamine-binding protein with simple models. Biophys J (2006) 0.93
Protein unfolding behavior studied by elastic network model. Biophys J (2008) 0.89
A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein. PLoS Comput Biol (2013) 0.88
Elastic Network Models are Robust to Variations in Formalism. J Chem Theory Comput (2012) 0.87
ALADYN: a web server for aligning proteins by matching their large-scale motion. Nucleic Acids Res (2010) 0.85
Dynamical basis for drug resistance of HIV-1 protease. BMC Struct Biol (2011) 0.85
Comparing interfacial dynamics in protein-protein complexes: an elastic network approach. BMC Struct Biol (2010) 0.85
Structural features that predict real-value fluctuations of globular proteins. Proteins (2012) 0.85
Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease. Biophys J (2010) 0.85
A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations. PLoS Comput Biol (2014) 0.84
cAMP Modulation of the cytoplasmic domain in the HCN2 channel investigated by molecular simulations. Biophys J (2006) 0.84
Coarse grained normal mode analysis vs. refined Gaussian Network Model for protein residue-level structural fluctuations. Bull Math Biol (2013) 0.84
Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles. J Chem Theory Comput (2013) 0.83
Protein flexibility prediction by an all-atom mean-field statistical theory. Protein Sci (2005) 0.82
Insight into the structure, dynamics and the unfolding property of amylosucrases: implications of rational engineering on thermostability. PLoS One (2012) 0.81
Temperature dependence of fluctuations in HIV1-protease. Eur Biophys J (2009) 0.81
Exploring the factors determining the dynamics of different protein folds. Protein Sci (2011) 0.80
Mechanism of cohesin loading onto chromosomes: a conformational dynamics study. Biophys J (2010) 0.80
Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments. Nucleic Acids Res (2015) 0.80
Structure-based simulations reveal concerted dynamics of GPCR activation. Proteins (2014) 0.79
Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition. PLoS Comput Biol (2013) 0.79
Models with energy penalty on interresidue rotation address insufficiencies of conventional elastic network models. Biophys J (2011) 0.79
Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution. Evol Appl (2015) 0.77
N-terminal myristoylation alters the calcium binding pathways in neuronal calcium sensor-1. J Biol Inorg Chem (2010) 0.77
Analysis of conformational motions and residue fluctuations for Escherichia coli ribose-binding protein revealed with elastic network models. Int J Mol Sci (2013) 0.76
Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution. PLoS One (2015) 0.76
How Intrinsic Molecular Dynamics Control Intramolecular Communication in Signal Transducers and Activators of Transcription Factor STAT5. PLoS One (2015) 0.75
Microscopic modeling of charge transport in sensing proteins. Nanoscale Res Lett (2012) 0.75
Separating the role of protein restraints and local metal-site interaction chemistry in the thermodynamics of a zinc finger protein. Biophys J (2011) 0.75
Unifying view of mechanical and functional hotspots across class A GPCRs. PLoS Comput Biol (2017) 0.75
B-factor Analysis and Conformational Rearrangement of Aldose Reductase. Curr Proteomics (2014) 0.75
Elastic network model of learned maintained contacts to predict protein motion. PLoS One (2017) 0.75
Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor. J Mol Model (2016) 0.75
A universal model for mobility and migration patterns. Nature (2012) 7.18
Global protein function prediction from protein-protein interaction networks. Nat Biotechnol (2003) 6.28
Neutral theory and relative species abundance in ecology. Nature (2003) 5.40
Density dependence explains tree species abundance and diversity in tropical forests. Nature (2005) 3.24
Supply-demand balance and metabolic scaling. Proc Natl Acad Sci U S A (2002) 3.10
Patterns of relative species abundance in rainforests and coral reefs. Nature (2007) 2.45
Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns. Proc Natl Acad Sci U S A (2006) 2.21
A backbone-based theory of protein folding. Proc Natl Acad Sci U S A (2006) 2.00
Emergence of structural and dynamical properties of ecological mutualistic networks. Nature (2013) 1.89
A general basis for quarter-power scaling in animals. Proc Natl Acad Sci U S A (2010) 1.63
Human mobility in a continuum approach. PLoS One (2013) 1.57
Insight into the structure of amyloid fibrils from the analysis of globular proteins. PLoS Comput Biol (2006) 1.55
Geometry and symmetry presculpt the free-energy landscape of proteins. Proc Natl Acad Sci U S A (2004) 1.55
Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations. Protein Sci (2002) 1.54
First-principles design of nanomachines. Proc Natl Acad Sci U S A (2009) 1.41
Dynamical evolution of ecosystems. Nature (2006) 1.40
Inferring species interactions in tropical forests. Proc Natl Acad Sci U S A (2009) 1.31
Non-neutral vegetation dynamics. PLoS One (2006) 1.30
Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility. Proc Natl Acad Sci U S A (2008) 1.25
Water-controlled wealth of nations. Proc Natl Acad Sci U S A (2013) 1.23
The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site. J Biol Chem (2007) 1.23
Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. J Mol Biol (2002) 1.22
Cross-scale ecological dynamics and microbial size spectra in marine ecosystems. Proc Biol Sci (2002) 1.22
Scaling body size fluctuations. Proc Natl Acad Sci U S A (2013) 1.18
Targeting biomolecular flexibility with metadynamics. Curr Opin Struct Biol (2010) 1.16
Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures. J Mol Biol (2002) 1.13
Physics of proteins. Annu Rev Biophys Biomol Struct (2007) 1.12
Polarization effects and charge transfer in the KcsA potassium channel. Biophys Chem (2006) 1.12
Insights into the binding of Phenyltiocarbamide (PTC) agonist to its target human TAS2R38 bitter receptor. PLoS One (2010) 1.12
Geometry and physics of proteins. Proteins (2002) 1.12
Spatial scaling in model plant communities. Phys Rev Lett (2005) 1.11
The intracellular antibody capture technology (IACT): towards a consensus sequence for intracellular antibodies. J Mol Biol (2002) 1.08
Scale invariance in the dynamics of spontaneous behavior. Proc Natl Acad Sci U S A (2012) 1.08
Solute-solvent charge transfer in aqueous solution. Chemphyschem (2005) 1.04
Network structures from selection principles. Phys Rev Lett (2004) 1.04
Potassium permeation through the KcsA channel: a density functional study. Biochim Biophys Acta (2002) 1.04
Scaling in ecosystems and the linkage of macroecological laws. Phys Rev Lett (2007) 1.04
Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases. J Am Chem Soc (2005) 1.03
Spatial effects on species persistence and implications for biodiversity. Proc Natl Acad Sci U S A (2011) 1.03
Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations. J Am Chem Soc (2009) 1.02
Ecology: Towards a theory of biodiversity. Nature (2009) 1.02
A structural model of agonist binding to the alpha3beta4 neuronal nicotinic receptor. Br J Pharmacol (2003) 1.02
Coarse-grained model of proteins incorporating atomistic detail of the active site. Phys Rev Lett (2005) 1.02
The C-terminal Src inhibitory kinase (Csk)-mediated tyrosine phosphorylation is a novel molecular mechanism to limit P2X3 receptor function in mouse sensory neurons. J Biol Chem (2009) 1.00
Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa. Proc Natl Acad Sci U S A (2006) 1.00
Self-similarity and scaling in forest communities. Proc Natl Acad Sci U S A (2010) 0.98
Stochastic model for the species abundance problem in an ecological community. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.98
Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots. Biophys J (2004) 0.97
Structural facets of disease-linked human prion protein mutants: a molecular dynamic study. Proteins (2010) 0.97
Common attributes of native-state structures of proteins, disordered proteins, and amyloid. Proc Natl Acad Sci U S A (2006) 0.97
Convergent dynamics in the protease enzymatic superfamily. J Am Chem Soc (2006) 0.97
On the oligomeric state of DJ-1 protein and its mutants associated with Parkinson Disease. A combined computational and in vitro study. J Biol Chem (2007) 0.97
Dynamics and energetics of water permeation through the aquaporin channel. Proteins (2004) 0.97
Maximum entropy approach for deducing amino Acid interactions in proteins. Phys Rev Lett (2008) 0.96
GOMoDo: A GPCRs online modeling and docking webserver. PLoS One (2013) 0.96
Inhibition of alpha-synuclein fibrillization by dopamine is mediated by interactions with five C-terminal residues and with E83 in the NAC region. PLoS One (2008) 0.95
Water-assisted reaction mechanism of monozinc beta-lactamases. J Am Chem Soc (2004) 0.94
Tetraethylammonium binding to the outer mouth of the KcsA potassium channel: implications for ion permeation. J Recept Signal Transduct Res (2002) 0.94
Common mechanistic features among metallo-beta-lactamases: a computational study of Aeromonas hydrophila CphA enzyme. J Biol Chem (2009) 0.94
Dissociation of minor groove binders from DNA: insights from metadynamics simulations. Nucleic Acids Res (2008) 0.94
Regulation of bestrophins by Ca2+: a theoretical and experimental study. PLoS One (2009) 0.93
Form, function, and evolution of living organisms. Proc Natl Acad Sci U S A (2014) 0.92
Structural motifs of biomolecules. Proc Natl Acad Sci U S A (2007) 0.91
Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases. J Am Chem Soc (2007) 0.91
Calculation of redox properties: understanding short- and long-range effects in rubredoxin. J Phys Chem B (2007) 0.91
Evolution and selection of river networks: statics, dynamics, and complexity. Proc Natl Acad Sci U S A (2014) 0.91
Exploring the universe of protein structures beyond the Protein Data Bank. PLoS Comput Biol (2010) 0.91
Species lifetime distribution for simple models of ecologies. Proc Natl Acad Sci U S A (2005) 0.90
Prediction of folding rates and transition-state placement from native-state geometry. Proteins (2003) 0.90
What can one learn from experiments about the elusive transition state? Protein Sci (2004) 0.90
Ontogenetic growth: Modelling universality and scaling. Nature (2002) 0.89
Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics. Biophys J (2010) 0.89
Common structural traits across pathogenic mutants of the human prion protein and their implications for familial prion diseases. J Mol Biol (2011) 0.89
Bioinorganic chemistry of Parkinson's disease: structural determinants for the copper-mediated amyloid formation of alpha-synuclein. Inorg Chem (2010) 0.89
Molecular modeling of ion channels: structural predictions. Curr Opin Chem Biol (2003) 0.89
A knowledge-based scale for amino acid membrane propensity. Proteins (2003) 0.89
Peptide aptamers targeting mutant p53 induce apoptosis in tumor cells. Cancer Res (2008) 0.88
Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase. Chemistry (2007) 0.88
Nicotine blocks the hyperpolarization-activated current Ih and severely impairs the oscillatory behavior of oriens-lacunosum moleculare interneurons. J Neurosci (2010) 0.88
Self-templated nucleation in peptide and protein aggregation. Phys Rev Lett (2008) 0.88
Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion. Proc Natl Acad Sci U S A (2012) 0.88
G protein inactive and active forms investigated by simulation methods. Proteins (2009) 0.88
Target-related applications of first principles quantum chemical methods in drug design. Chem Rev (2006) 0.88
Assembly of protein tertiary structures from secondary structures using optimized potentials. Proteins (2003) 0.88
Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding. PLoS One (2013) 0.87
Crucial stages of protein folding through a solvable model: predicting target sites for enzyme-inhibiting drugs. Protein Sci (2002) 0.87
Molecular dynamics study of the KcsA channel at 2.0-A resolution: stability and concerted motions within the pore. Biochim Biophys Acta (2004) 0.87
Enzymatic GTP hydrolysis: insights from an ab initio molecular dynamics study. J Am Chem Soc (2002) 0.87
Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Curr Opin Struct Biol (2007) 0.87
Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes. PLoS One (2012) 0.86
Origin of functional diversity among tetrameric voltage-gated channels. Proteins (2007) 0.86
An allometry-based approach for understanding forest structure, predicting tree-size distribution and assessing the degree of disturbance. Proc Biol Sci (2013) 0.86
Folding pathways of prion and doppel. Biophys J (2002) 0.86
On the zwitterionic nature of gas-phase peptides and protein ions. PLoS Comput Biol (2010) 0.86
Mechanism of action of cyclophilin a explored by metadynamics simulations. PLoS Comput Biol (2009) 0.86
Calcium binding to the transmembrane domain of the sarcoplasmic reticulum Ca2+-ATPase: insights from molecular modeling. Proteins (2003) 0.85
Ligand specificity of odorant receptors. J Mol Model (2006) 0.85
Unified perspective on proteins: a physics approach. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.85
Organization of ecosystems in the vicinity of a novel phase transition. Phys Rev Lett (2004) 0.85