PubRank

Nikolay V Dokholyan

Author PubWeight™ 153.00‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function. Proc Natl Acad Sci U S A 2008 3.08
2 Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA 2008 2.86
3 Eris: an automated estimator of protein stability. Nat Methods 2007 2.78
4 Engineered allosteric activation of kinases in living cells. Nat Biotechnol 2010 2.44
5 Emergence of protein fold families through rational design. PLoS Comput Biol 2006 2.35
6 Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure 2008 2.22
7 Outcome of a workshop on applications of protein models in biomedical research. Structure 2009 2.05
8 iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics 2008 2.03
9 RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA 2012 1.88
10 Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol 2003 1.80
11 Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J Mol Biol 2002 1.66
12 Modeling backbone flexibility improves protein stability estimation. Structure 2007 1.65
13 Automated minimization of steric clashes in protein structures. Proteins 2011 1.64
14 Multiscale modeling of nucleosome dynamics. Biophys J 2006 1.63
15 Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating. J Biol Chem 2008 1.62
16 On the significance of an RNA tertiary structure prediction. RNA 2010 1.61
17 Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J 2002 1.55
18 The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 2012 1.54
19 Computational design of a PAK1 binding protein. J Mol Biol 2010 1.51
20 Mechanism for the alpha-helix to beta-hairpin transition. Proteins 2003 1.51
21 The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis. Proc Natl Acad Sci U S A 2004 1.46
22 Modifications of superoxide dismutase (SOD1) in human erythrocytes: a possible role in amyotrophic lateral sclerosis. J Biol Chem 2009 1.46
23 Can contact potentials reliably predict stability of proteins? J Mol Biol 2004 1.44
24 Simple but predictive protein models. Trends Biotechnol 2005 1.39
25 MedusaScore: an accurate force field-based scoring function for virtual drug screening. J Chem Inf Model 2008 1.37
26 Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc 2009 1.33
27 Regulatory insertion removal restores maturation, stability and function of DeltaF508 CFTR. J Mol Biol 2010 1.31
28 Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. Biophys J 2004 1.29
29 Fast complementation of split fluorescent protein triggered by DNA hybridization. Proc Natl Acad Sci U S A 2006 1.26
30 Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants. Proc Natl Acad Sci U S A 2006 1.25
31 Imprint of evolution on protein structures. Proc Natl Acad Sci U S A 2004 1.24
32 Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation. Proc Natl Acad Sci U S A 2008 1.23
33 Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP. J Am Chem Soc 2010 1.23
34 The path of DNA in the kinetochore. Curr Biol 2006 1.22
35 Rapid flexible docking using a stochastic rotamer library of ligands. J Chem Inf Model 2010 1.21
36 Three-dimensional RNA structure refinement by hydroxyl radical probing. Nat Methods 2012 1.20
37 Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. J Mol Biol 2005 1.18
38 Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR. J Mol Biol 2012 1.18
39 Protein folding: then and now. Arch Biochem Biophys 2007 1.18
40 Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis. J Mol Biol 2003 1.17
41 Molecular origin of polyglutamine aggregation in neurodegenerative diseases. PLoS Comput Biol 2005 1.17
42 Polyglutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences. PLoS Comput Biol 2010 1.17
43 BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics. Mol Cell Proteomics 2008 1.17
44 Correctors of ΔF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein. FASEB J 2012 1.17
45 Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry 2013 1.16
46 iFold: a platform for interactive folding simulations of proteins. Bioinformatics 2006 1.15
47 Topological determinants of protein domain swapping. Structure 2006 1.15
48 Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. J Phys Chem B 2012 1.14
49 Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry 2010 1.13
50 Deciphering protein dynamics from NMR data using explicit structure sampling and selection. Biophys J 2007 1.13
51 Active nuclear receptors exhibit highly correlated AF-2 domain motions. PLoS Comput Biol 2008 1.12
52 New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate. Structure 2004 1.11
53 The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet 2006 1.10
54 Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding. PLoS Comput Biol 2008 1.08
55 Regulation of the epithelial Na+ channel and airway surface liquid volume by serine proteases. Pflugers Arch 2010 1.08
56 Rational design of a ligand-controlled protein conformational switch. Proc Natl Acad Sci U S A 2013 1.08
57 Fidelity of the protein structure reconstruction from inter-residue proximity constraints. J Phys Chem B 2007 1.06
58 The complex molecular biology of amyotrophic lateral sclerosis (ALS). Prog Mol Biol Transl Sci 2012 1.05
59 Fast screening of protein surfaces using geometric invariant fingerprints. Proc Natl Acad Sci U S A 2009 1.05
60 Structural and dynamic determinants of protein-peptide recognition. Structure 2011 1.04
61 Harnessing a physiologic mechanism for siRNA delivery with mimetic lipoprotein particles. Mol Ther 2012 1.04
62 Structural determinants of skeletal muscle ryanodine receptor gating. J Biol Chem 2013 1.03
63 Insights into allosteric control of vinculin function from its large scale conformational dynamics. J Biol Chem 2006 1.03
64 Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR. J Mol Biol 2008 1.01
65 A single disulfide bond differentiates aggregation pathways of beta2-microglobulin. J Mol Biol 2005 1.01
66 Glutathionylation at Cys-111 induces dissociation of wild type and FALS mutant SOD1 dimers. Biochemistry 2011 1.00
67 Identification of a consensus motif in substrates bound by a Type I Hsp40. Proc Natl Acad Sci U S A 2009 1.00
68 Scaling behavior and structure of denatured proteins. Structure 2005 1.00
69 Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm. Mol Biol Evol 2008 0.99
70 Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. J Mol Biol 2002 0.99
71 Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant. Nucleic Acids Res 2011 0.99
72 Using protein design for homology detection and active site searches. Proc Natl Acad Sci U S A 2003 0.99
73 Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics. J Mol Biol 2007 0.99
74 A structural model reveals energy transduction in dynein. Proc Natl Acad Sci U S A 2006 0.98
75 FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis. Amyloid 2006 0.98
76 Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers. PLoS Comput Biol 2008 0.97
77 Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase. J Mol Biol 2011 0.97
78 Local unfolding of Cu, Zn superoxide dismutase monomer determines the morphology of fibrillar aggregates. J Mol Biol 2011 0.96
79 Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation. Proteins 2005 0.96
80 Direct observation of protein folding, aggregation, and a prion-like conformational conversion. J Biol Chem 2005 0.96
81 The length dependence of the polyQ-mediated protein aggregation. J Biol Chem 2007 0.95
82 A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1). PLoS Comput Biol 2009 0.94
83 Gaia: automated quality assessment of protein structure models. Bioinformatics 2011 0.94
84 Kinetic models for the coordinated stepping of cytoplasmic dynein. J Chem Phys 2009 0.94
85 Knowledge-based design of a biosensor to quantify localized ERK activation in living cells. Chem Biol 2013 0.93
86 Protein evolution within a structural space. Biophys J 2003 0.92
87 Interaction with the 5D3 monoclonal antibody is regulated by intramolecular rearrangements but not by covalent dimer formation of the human ABCG2 multidrug transporter. J Biol Chem 2008 0.91
88 Multiple folding pathways of the SH3 domain. Biophys J 2004 0.91
89 Rigid substructure search. Bioinformatics 2011 0.91
90 G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase. J Biol Chem 2009 0.91
91 Serotonin-induced hypersensitivity via inhibition of catechol O-methyltransferase activity. Mol Pain 2012 0.90
92 ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions. Biochim Biophys Acta 2011 0.89
93 Possible mechanism for cold denaturation of proteins at high pressure. Phys Rev Lett 2003 0.88
94 Combined application of cheminformatics- and physical force field-based scoring functions improves binding affinity prediction for CSAR data sets. J Chem Inf Model 2011 0.88
95 Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics. Biophys J 2013 0.87
96 N-terminal strands of filamin Ig domains act as a conformational switch under biological forces. Proteins 2010 0.87
97 Energetic and structural basis for activation of the epithelial sodium channel by matriptase. Biochemistry 2012 0.87
98 Probing protein aggregation using discrete molecular dynamics. Front Biosci 2008 0.86
99 Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets. Biophys J 2012 0.86
100 New models of Tetrahymena telomerase RNA from experimentally derived constraints and modeling. J Am Chem Soc 2012 0.86
101 Statistical analysis of SHAPE-directed RNA secondary structure modeling. Biochemistry 2013 0.85
102 Structural mechanism of S-adenosyl methionine binding to catechol O-methyltransferase. PLoS One 2011 0.85
103 Non-native soluble oligomers of Cu/Zn superoxide dismutase (SOD1) contain a conformational epitope linked to cytotoxicity in amyotrophic lateral sclerosis (ALS). Biochemistry 2014 0.85
104 Molecular mechanisms of polypeptide aggregation in human diseases. Curr Protein Pept Sci 2007 0.85
105 Identification of novel integrin binding partners for calcium and integrin binding protein 1 (CIB1): structural and thermodynamic basis of CIB1 promiscuity. Biochemistry 2013 0.84
106 Cheminformatics meets molecular mechanics: a combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening. J Chem Inf Model 2011 0.83
107 Dynamics intrinsic to cystic fibrosis transmembrane conductance regulator function and stability. Cold Spring Harb Perspect Med 2013 0.83
108 Multiscale approaches for studying energy transduction in dynein. Phys Chem Chem Phys 2009 0.83
109 Structural basis for the sequence-dependent effects of platinum-DNA adducts. Nucleic Acids Res 2009 0.83
110 Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity. Phys Chem Chem Phys 2010 0.83
111 Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark. J Chem Inf Model 2012 0.83
112 Isoform divergence of the filamin family of proteins. Mol Biol Evol 2009 0.82
113 Regioselectivity of Catechol O-Methyltransferase Confers Enhancement of Catalytic Activity. Chem Phys Lett 2011 0.81
114 Structural basis for μ-opioid receptor binding and activation. Structure 2011 0.81
115 Fingerprint-based structure retrieval using electron density. Proteins 2011 0.81
116 Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels. Proteins 2009 0.81
117 Hybrid dynamics simulation engine for metalloproteins. Biophys J 2012 0.80
118 A didactic model of macromolecular crowding effects on protein folding. PLoS One 2010 0.80
119 Light-cleavable rapamycin dimer as an optical trigger for protein dimerization. Chem Commun (Camb) 2015 0.79
120 The evolution dynamics of model proteins. J Chem Phys 2004 0.79
121 Flanking bases influence the nature of DNA distortion by platinum 1,2-intrastrand (GG) cross-links. PLoS One 2011 0.79
122 The maturation of HIV-1 protease precursor studied by discrete molecular dynamics. Proteins 2013 0.79
123 Computational evaluation of protein stability change upon mutations. Methods Mol Biol 2010 0.78
124 Insights into thermophilic archaebacterial membrane stability from simplified models of lipid membranes. Phys Rev E Stat Nonlin Soft Matter Phys 2007 0.78
125 Predicting binding affinity of CSAR ligands using both structure-based and ligand-based approaches. J Chem Inf Model 2013 0.77
126 RNA tertiary structure analysis by 2'-hydroxyl molecular interference. Biochemistry 2014 0.77
127 Thermodynamic stability of histone H3 is a necessary but not sufficient driving force for its evolutionary conservation. PLoS Comput Biol 2011 0.77
128 Highly covarying residues have a functional role in antibody constant domains. Proteins 2013 0.77
129 DNA sequence mediates nucleosome structure and stability. Biophys J 2007 0.77
130 A physical model reveals the mechanochemistry responsible for dynein's processive motion. Biophys J 2011 0.77
131 A folding pathway-dependent score to recognize membrane proteins. PLoS One 2011 0.76
132 Intra- and inter-subunit disulfide bond formation is nonessential in adeno-associated viral capsids. PLoS One 2012 0.76
133 COMT gene locus: new functional variants. Pain 2015 0.75
134 Approaches for probing the sequence space of substrates recognized by molecular chaperones. Methods 2010 0.75
135 Thermal unfolding pathway of PHD2 catalytic domain in three different PHD2 species: computational approaches. PLoS One 2012 0.75
136 Combining fluorescence detection and mass spectrometric analysis for comprehensive and quantitative analysis of redox-sensitive cysteines in native membrane proteins. Anal Chem 2006 0.75
137 Computational approaches to understanding protein aggregation in neurodegeneration. J Mol Cell Biol 2014 0.75
138 Postbreakthrough behavior in flow through porous media. Phys Rev E Stat Nonlin Soft Matter Phys 2003 0.75
139 Recognition of platinum-DNA adducts by HMGB1a. Biochemistry 2012 0.75
140 Protein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family. Acta Crystallogr D Biol Crystallogr 2013 0.75
141 Molecular modeling tools and approaches for CFTR and cystic fibrosis. Methods Mol Biol 2011 0.75
142 Engineering Pak1 Allosteric Switches. ACS Synth Biol 2017 0.75
143 Corrigendum: Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins. Sci Rep 2017 0.75
144 Corrigendum: Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins. Sci Rep 2017 0.75
145 Metric to distinguish closely related domain families using sequence information. J Mol Biol 2012 0.75