Published in Proteins on February 01, 2007
Improved prediction of protein side-chain conformations with SCWRL4. Proteins (2009) 5.67
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure (2011) 2.61
Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci (2010) 2.16
Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nat Chem (2014) 1.67
Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model. PLoS Comput Biol (2010) 1.44
Salt bridges: geometrically specific, designable interactions. Proteins (2011) 1.39
Shape shifting leads to small-molecule allosteric drug discovery. Chem Biol (2008) 1.27
The Dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water. Protein Sci (2011) 1.16
The missing link in plant histidine biosynthesis: Arabidopsis myoinositol monophosphatase-like2 encodes a functional histidinol-phosphate phosphatase. Plant Physiol (2009) 0.94
Development of a rotamer library for use in beta-peptide foldamer computational design. J Am Chem Soc (2010) 0.93
Identification of a novel LXXLL motif in α-actinin 4-spliced isoform that is critical for its interaction with estrogen receptor α and co-activators. J Biol Chem (2012) 0.93
Modeling mutations in protein structures. Protein Sci (2007) 0.92
E pluribus unum, no more: from one crystal, many conformations. Curr Opin Struct Biol (2014) 0.91
Fine grained sampling of residue characteristics using molecular dynamics simulation. Comput Biol Chem (2010) 0.87
TAP score: torsion angle propensity normalization applied to local protein structure evaluation. BMC Bioinformatics (2007) 0.87
Side-chain conformational heterogeneity of intermediates in the Escherichia coli dihydrofolate reductase catalytic cycle. Biochemistry (2013) 0.83
The role of atomic level steric effects and attractive forces in protein folding. Proteins (2011) 0.83
Routine phasing of coiled-coil protein crystal structures with AMPLE. IUCrJ (2015) 0.82
Enhancing human spermine synthase activity by engineered mutations. PLoS Comput Biol (2013) 0.82
Molprobity's ultimate rotamer-library distributions for model validation. Proteins (2016) 0.80
Structure of the Escherichia coli RNA polymerase alpha subunit C-terminal domain. Acta Crystallogr D Biol Crystallogr (2010) 0.79
Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds. IUCrJ (2016) 0.77
Effect of short- and long-range interactions on trp rotamer populations determined by site-directed tryptophan fluorescence of tear lipocalin. PLoS One (2013) 0.76
Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences. J Am Chem Soc (2016) 0.75
PISCES: a protein sequence culling server. Bioinformatics (2003) 11.87
A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003) 9.25
Improved prediction of protein side-chain conformations with SCWRL4. Proteins (2009) 5.67
Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev Cell (2005) 4.83
Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci (2003) 4.82
PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta (2010) 3.62
PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res (2005) 3.55
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure (2011) 2.61
CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins (2003) 2.60
Conformation dependence of backbone geometry in proteins. Structure (2009) 2.33
Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation. Proc Natl Acad Sci U S A (2010) 1.87
Aurora A kinase (AURKA) in normal and pathological cell division. Cell Mol Life Sci (2012) 1.84
A new clustering of antibody CDR loop conformations. J Mol Biol (2010) 1.83
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. Bioinformatics (2012) 1.82
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. Nat Protoc (2008) 1.79
Scoring profile-to-profile sequence alignments. Protein Sci (2004) 1.71
Assessment of disorder predictions in CASP6. Proteins (2005) 1.69
Promotion of tumor growth by murine fibroblast activation protein, a serine protease, in an animal model. Cancer Res (2002) 1.66
Statistical analysis of interface similarity in crystals of homologous proteins. J Mol Biol (2008) 1.55
Oligomerization of BAK by p53 utilizes conserved residues of the p53 DNA binding domain. J Biol Chem (2008) 1.55
Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model. PLoS Comput Biol (2010) 1.44
Assessment of fold recognition predictions in CASP6. Proteins (2005) 1.41
MollDE: a homology modeling framework you can click with. Bioinformatics (2005) 1.40
The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms. Nucleic Acids Res (2010) 1.30
Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc Natl Acad Sci U S A (2011) 1.23
BioDownloader: bioinformatics downloads and updates in a few clicks. Bioinformatics (2007) 1.14
A modified HSP70 inhibitor shows broad activity as an anticancer agent. Mol Cancer Res (2013) 1.14
A new model for allosteric regulation of phenylalanine hydroxylase: implications for disease and therapeutics. Arch Biochem Biophys (2013) 1.11
ProtBuD: a database of biological unit structures of protein families and superfamilies. Bioinformatics (2006) 1.09
The role of balanced training and testing data sets for binary classifiers in bioinformatics. PLoS One (2013) 1.09
Domain definition and target classification for CASP6. Proteins (2005) 1.06
A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions. Acta Crystallogr D Biol Crystallogr (2008) 1.05
Minimal ensembles of side chain conformers for modeling protein-protein interactions. Proteins (2011) 1.03
Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase. Proteins (2010) 1.03
Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization. Methods Mol Biol (2012) 1.02
CD45-deficient severe combined immunodeficiency caused by uniparental disomy. Proc Natl Acad Sci U S A (2012) 0.99
Rapid calcium-dependent activation of Aurora-A kinase. Nat Commun (2010) 0.98
Development of a rotamer library for use in beta-peptide foldamer computational design. J Am Chem Soc (2010) 0.93
Prediction of phenotypes of missense mutations in human proteins from biological assemblies. Proteins (2012) 0.92
Clinical trials that explicitly exclude gay and lesbian patients. N Engl J Med (2010) 0.92
The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite. PLoS One (2013) 0.91
An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases. Proteins (2009) 0.88
Architecture and assembly of HIV integrase multimers in the absence of DNA substrates. J Biol Chem (2013) 0.87
Charge asymmetry in the proteins of the outer membrane. Bioinformatics (2013) 0.86
Protein-intrinsic and signaling network-based sources of resistance to EGFR- and ErbB family-targeted therapies in head and neck cancer. Drug Resist Updat (2011) 0.86
A structural basis for half-of-the-sites metal binding revealed in Drosophila melanogaster porphobilinogen synthase. J Biol Chem (2003) 0.86
Identification and characterization of a paralog of human cell cycle checkpoint gene HUS1. Genomics (2002) 0.86
Mapping the epitope of an inhibitory monoclonal antibody to the C-terminal DNA-binding domain of HIV-1 integrase. J Biol Chem (2002) 0.82
A highly selective dual insulin receptor (IR)/insulin-like growth factor 1 receptor (IGF-1R) inhibitor derived from an extracellular signal-regulated kinase (ERK) inhibitor. J Biol Chem (2013) 0.82
CASA: a server for the critical assessment of protein sequence alignment accuracy. Bioinformatics (2002) 0.80
Issues in interpreting the in vivo activity of Aurora-A. Expert Opin Ther Targets (2014) 0.80
OVCA2 is downregulated and degraded during retinoid-induced apoptosis. Int J Cancer (2002) 0.79
Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. J Med Chem (2014) 0.78
Acetylation of the transcriptional repressor Ume6p allows efficient promoter release and timely induction of the meiotic transient transcription program in yeast. Mol Cell Biol (2013) 0.77
The Rosetta all-atom energy function for macromolecular modeling and design. J Chem Theory Comput (2017) 0.76
An Integrated Database for Complex Protein Structure Modeling. Proceedings (IEEE Int Conf Bioinformatics Biomed) (2008) 0.75