Published in Proc Natl Acad Sci U S A on September 17, 2009
On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface (2012) 1.16
PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res (2011) 0.91
Rigid substructure search. Bioinformatics (2011) 0.91
Beauty is in the eye of the beholder: proteins can recognize binding sites of homologous proteins in more than one way. PLoS Comput Biol (2010) 0.87
Pocket-based drug design: exploring pocket space. AAPS J (2012) 0.86
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. Nucleic Acids Res (2014) 0.84
Fingerprint-based structure retrieval using electron density. Proteins (2011) 0.81
Protein surface characterization using an invariant descriptor. Int J Biomed Imaging (2011) 0.76
Proteochemometric modeling of the antigen-antibody interaction: new fingerprints for antigen, antibody and epitope-paratope interaction. PLoS One (2015) 0.76
PBSword: a web server for searching similar protein-protein binding sites. Nucleic Acids Res (2012) 0.75
A local average distance descriptor for flexible protein structure comparison. BMC Bioinformatics (2014) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A (1988) 193.60
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
Protein structure comparison by alignment of distance matrices. J Mol Biol (1993) 34.74
TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15
Reduced surface: an efficient way to compute molecular surfaces. Biopolymers (1996) 10.62
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A (1992) 6.86
One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol (2002) 3.88
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci (1997) 3.50
Catalytic triads and their relatives. Trends Biochem Sci (1998) 3.06
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci (2003) 2.98
A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol (2002) 2.79
Recognition of functional sites in protein structures. J Mol Biol (2004) 2.32
Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc Natl Acad Sci U S A (1991) 2.26
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics (2005) 1.97
Inferring functional relationships of proteins from local sequence and spatial surface patterns. J Mol Biol (2003) 1.96
A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J Mol Biol (1994) 1.88
Understanding hierarchical protein evolution from first principles. J Mol Biol (2001) 1.62
Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins (2008) 1.60
Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships. J Mol Biol (2005) 1.46
Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching. Proteins (2004) 1.34
A fourier fingerprint-based method for protein surface representation. J Chem Inf Model (2005) 0.87
Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E. Cell (2003) 3.46
The PHD finger of the chromatin-associated protein ING2 functions as a nuclear phosphoinositide receptor. Cell (2003) 3.36
Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J Biol Chem (2006) 3.14
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
Small-molecule inhibition of TNF-alpha. Science (2005) 1.83
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
Effect of surface treatment on diffusion and domain formation in supported lipid bilayers. Biophys J (2007) 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
Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis. J Mol Biol (2003) 1.17
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
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
Regulation of the epithelial Na+ channel and airway surface liquid volume by serine proteases. Pflugers Arch (2010) 1.08
Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding. PLoS Comput Biol (2008) 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
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
CTL recognition of a protective immunodominant influenza A virus nucleoprotein epitope utilizes a highly restricted Vbeta but diverse Valpha repertoire: functional and structural implications. J Mol Biol (2007) 1.01
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
Scaling behavior and structure of denatured proteins. Structure (2005) 1.00
Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm. Mol Biol Evol (2008) 0.99
Using protein design for homology detection and active site searches. Proc Natl Acad Sci U S A (2003) 0.99
Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. J Mol Biol (2002) 0.99
Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant. Nucleic Acids Res (2011) 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
Rapid optimization and prototyping for therapeutic antibody-like molecules. MAbs (2013) 0.93
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
MM-141, an IGF-IR- and ErbB3-directed bispecific antibody, overcomes network adaptations that limit activity of IGF-IR inhibitors. Mol Cancer Ther (2013) 0.91
Rigid substructure search. Bioinformatics (2011) 0.91
G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase. J Biol Chem (2009) 0.91
Conserved amino acid networks involved in antibody variable domain interactions. Proteins (2009) 0.90