Published in Structure on July 01, 2005
Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy. Proc Natl Acad Sci U S A (2006) 2.48
Folding versus aggregation: polypeptide conformations on competing pathways. Arch Biochem Biophys (2007) 1.97
Multiscale modeling of nucleosome dynamics. Biophys J (2006) 1.63
Quantitative characterization of intrinsic disorder in polyglutamine: insights from analysis based on polymer theories. Biophys J (2007) 1.53
Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions. Biophys J (2006) 1.21
Protein folding: then and now. Arch Biochem Biophys (2007) 1.18
Describing sequence-ensemble relationships for intrinsically disordered proteins. Biochem J (2013) 1.00
Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure. Proc Natl Acad Sci U S A (2013) 0.96
Denaturant-induced expansion and compaction of a multi-domain protein: IgG. J Mol Biol (2008) 0.89
Small-angle X-ray scattering of reduced ribonuclease A: effects of solution conditions and comparisons with a computational model of unfolded proteins. J Mol Biol (2008) 0.89
A self-consistent description of the conformational behavior of chemically denatured proteins from NMR and small angle scattering. Biophys J (2009) 0.89
Multiscale approaches for studying energy transduction in dynein. Phys Chem Chem Phys (2009) 0.83
Insights into protein aggregation by NMR characterization of insoluble SH3 mutants solubilized in salt-free water. PLoS One (2009) 0.83
Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling. Chem Rev (2016) 0.82
Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series. Biophys J (2016) 0.76
Characterization of the unfolded state of repeat proteins. HFSP J (2008) 0.75
An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations. Biophys J (2017) 0.75
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
Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA (2008) 2.86
Eris: an automated estimator of protein stability. Nat Methods (2007) 2.78
Engineered allosteric activation of kinases in living cells. Nat Biotechnol (2010) 2.44
Emergence of protein fold families through rational design. PLoS Comput Biol (2006) 2.35
Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure (2008) 2.22
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics (2008) 2.03
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88
Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol (2003) 1.80
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J Mol Biol (2002) 1.66
Modeling backbone flexibility improves protein stability estimation. Structure (2007) 1.65
Automated minimization of steric clashes in protein structures. Proteins (2011) 1.64
Multiscale modeling of nucleosome dynamics. Biophys J (2006) 1.63
Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating. J Biol Chem (2008) 1.62
On the significance of an RNA tertiary structure prediction. RNA (2010) 1.61
Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J (2002) 1.55
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Computational design of a PAK1 binding protein. J Mol Biol (2010) 1.51
Mechanism for the alpha-helix to beta-hairpin transition. Proteins (2003) 1.51
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
Modifications of superoxide dismutase (SOD1) in human erythrocytes: a possible role in amyotrophic lateral sclerosis. J Biol Chem (2009) 1.46
Can contact potentials reliably predict stability of proteins? J Mol Biol (2004) 1.44
Simple but predictive protein models. Trends Biotechnol (2005) 1.39
MedusaScore: an accurate force field-based scoring function for virtual drug screening. J Chem Inf Model (2008) 1.37
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc (2009) 1.33
Regulatory insertion removal restores maturation, stability and function of DeltaF508 CFTR. J Mol Biol (2010) 1.31
Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. Biophys J (2004) 1.29
Fast complementation of split fluorescent protein triggered by DNA hybridization. Proc Natl Acad Sci U S A (2006) 1.26
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
Imprint of evolution on protein structures. Proc Natl Acad Sci U S A (2004) 1.24
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
Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP. J Am Chem Soc (2010) 1.23
The path of DNA in the kinetochore. Curr Biol (2006) 1.22
Rapid flexible docking using a stochastic rotamer library of ligands. J Chem Inf Model (2010) 1.21
Three-dimensional RNA structure refinement by hydroxyl radical probing. Nat Methods (2012) 1.20
Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. J Mol Biol (2005) 1.18
Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR. J Mol Biol (2012) 1.18
Protein folding: then and now. Arch Biochem Biophys (2007) 1.18
BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics. Mol Cell Proteomics (2008) 1.17
Polyglutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences. PLoS Comput Biol (2010) 1.17
Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis. J Mol Biol (2003) 1.17
Molecular origin of polyglutamine aggregation in neurodegenerative diseases. PLoS Comput Biol (2005) 1.17
Correctors of ΔF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein. FASEB J (2012) 1.17
Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry (2013) 1.16
iFold: a platform for interactive folding simulations of proteins. Bioinformatics (2006) 1.15
Topological determinants of protein domain swapping. Structure (2006) 1.15
Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. J Phys Chem B (2012) 1.14
Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry (2010) 1.13
Deciphering protein dynamics from NMR data using explicit structure sampling and selection. Biophys J (2007) 1.13
Active nuclear receptors exhibit highly correlated AF-2 domain motions. PLoS Comput Biol (2008) 1.12
New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate. Structure (2004) 1.11
The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet (2006) 1.10
Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding. PLoS Comput Biol (2008) 1.08
Regulation of the epithelial Na+ channel and airway surface liquid volume by serine proteases. Pflugers Arch (2010) 1.08
Rational design of a ligand-controlled protein conformational switch. Proc Natl Acad Sci U S A (2013) 1.08
Fidelity of the protein structure reconstruction from inter-residue proximity constraints. J Phys Chem B (2007) 1.06
The complex molecular biology of amyotrophic lateral sclerosis (ALS). Prog Mol Biol Transl Sci (2012) 1.05
Fast screening of protein surfaces using geometric invariant fingerprints. Proc Natl Acad Sci U S A (2009) 1.05
Structural and dynamic determinants of protein-peptide recognition. Structure (2011) 1.04
Harnessing a physiologic mechanism for siRNA delivery with mimetic lipoprotein particles. Mol Ther (2012) 1.04
Structural determinants of skeletal muscle ryanodine receptor gating. J Biol Chem (2013) 1.03
Insights into allosteric control of vinculin function from its large scale conformational dynamics. J Biol Chem (2006) 1.03
Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR. J Mol Biol (2008) 1.01
A single disulfide bond differentiates aggregation pathways of beta2-microglobulin. J Mol Biol (2005) 1.01
Identification of a consensus motif in substrates bound by a Type I Hsp40. Proc Natl Acad Sci U S A (2009) 1.00
Glutathionylation at Cys-111 induces dissociation of wild type and FALS mutant SOD1 dimers. Biochemistry (2011) 1.00
Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm. Mol Biol Evol (2008) 0.99
Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant. Nucleic Acids Res (2011) 0.99
Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. J Mol Biol (2002) 0.99
Using protein design for homology detection and active site searches. Proc Natl Acad Sci U S A (2003) 0.99
Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics. J Mol Biol (2007) 0.99
A structural model reveals energy transduction in dynein. Proc Natl Acad Sci U S A (2006) 0.98
FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis. Amyloid (2006) 0.98
Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase. J Mol Biol (2011) 0.97
Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers. PLoS Comput Biol (2008) 0.97
Local unfolding of Cu, Zn superoxide dismutase monomer determines the morphology of fibrillar aggregates. J Mol Biol (2011) 0.96
Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation. Proteins (2005) 0.96
Direct observation of protein folding, aggregation, and a prion-like conformational conversion. J Biol Chem (2005) 0.96
The length dependence of the polyQ-mediated protein aggregation. J Biol Chem (2007) 0.95
A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1). PLoS Comput Biol (2009) 0.94
Gaia: automated quality assessment of protein structure models. Bioinformatics (2011) 0.94
Kinetic models for the coordinated stepping of cytoplasmic dynein. J Chem Phys (2009) 0.94
Knowledge-based design of a biosensor to quantify localized ERK activation in living cells. Chem Biol (2013) 0.93
Protein evolution within a structural space. Biophys J (2003) 0.92
Multiple folding pathways of the SH3 domain. Biophys J (2004) 0.91
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
G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase. J Biol Chem (2009) 0.91
Rigid substructure search. Bioinformatics (2011) 0.91
Serotonin-induced hypersensitivity via inhibition of catechol O-methyltransferase activity. Mol Pain (2012) 0.90
A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes. BMC Genomics (2014) 0.90
ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions. Biochim Biophys Acta (2011) 0.89
Possible mechanism for cold denaturation of proteins at high pressure. Phys Rev Lett (2003) 0.88
Scintillation proximity assay for inhibitors of Escherichia coli MurG and, optionally, MraY. Antimicrob Agents Chemother (2005) 0.88
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
Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics. Biophys J (2013) 0.87
Energetic and structural basis for activation of the epithelial sodium channel by matriptase. Biochemistry (2012) 0.87
N-terminal strands of filamin Ig domains act as a conformational switch under biological forces. Proteins (2010) 0.87
Probing protein aggregation using discrete molecular dynamics. Front Biosci (2008) 0.86
Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets. Biophys J (2012) 0.86