Published in PLoS Comput Biol on April 29, 2010
A new clustering of antibody CDR loop conformations. J Mol Biol (2010) 1.83
The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins. J Chem Theory Comput (2013) 1.65
Genomics-aided structure prediction. Proc Natl Acad Sci U S A (2012) 1.63
Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH. J Biomol NMR (2011) 1.51
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution. J Biomol NMR (2011) 1.38
Protein loop modeling by using fragment assembly and analytical loop closure. Proteins (2010) 1.25
Improvements to robotics-inspired conformational sampling in rosetta. PLoS One (2013) 1.18
Automated real-space refinement of protein structures using a realistic backbone move set. Biophys J (2011) 1.16
Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization. Proteins (2014) 1.05
Conversion of the enzyme guanylate kinase into a mitotic-spindle orienting protein by a single mutation that inhibits GMP-induced closing. Proc Natl Acad Sci U S A (2011) 0.90
(φ,ψ)₂ motifs: a purely conformation-based fine-grained enumeration of protein parts at the two-residue level. J Mol Biol (2011) 0.89
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations. Proc Natl Acad Sci U S A (2014) 0.85
Dock 'n roll: folding of a silk-inspired polypeptide into an amyloid-like beta solenoid. Soft Matter (2016) 0.82
Retrieving backbone string neighbors provides insights into structural modeling of membrane proteins. Mol Cell Proteomics (2012) 0.81
Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field. J Chem Theory Comput (2015) 0.80
Crystallographic model validation: from diagnosis to healing. Curr Opin Struct Biol (2013) 0.79
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. Elife (2016) 0.79
RCD+: Fast loop modeling server. Nucleic Acids Res (2016) 0.78
Chemical shift prediction for denatured proteins. J Biomol NMR (2013) 0.77
Deriving high-resolution protein backbone structure propensities from all crystal data using the information maximization device. PLoS One (2014) 0.77
Bayesian weighting of statistical potentials in NMR structure calculation. PLoS One (2014) 0.77
Accurate Structure Prediction of CDR H3 Loops Enabled by a Novel Structure-Based C-Terminal Constraint. J Immunol (2016) 0.76
Beyond basins: φ,ψ preferences of a residue depend heavily on the φ,ψ values of its neighbors. Protein Sci (2016) 0.75
Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core. Proc Natl Acad Sci U S A (2017) 0.75
Residue-centric modeling and design of saccharide and glycoconjugate structures. J Comput Chem (2016) 0.75
Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model. J Chem Theory Comput (2016) 0.75
Profile of Michael I. Jordan. Proc Natl Acad Sci U S A (2013) 0.75
Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions. Comput Struct Biotechnol J (2017) 0.75
Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins. J Biol Phys (2017) 0.75
Improving hybrid statistical and physical forcefields through local structure enumeration. Protein Sci (2016) 0.75
Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding. J Biomol Struct Dyn (2014) 0.75
Stability engineering of anti-EGFR scFv antibodies by rational design of a lambda-to-kappa swap of the VL framework using a structure-guided approach. MAbs (2015) 0.75
A closer look into the α-helix basin. Sci Rep (2016) 0.75
Decrypting Strong and Weak Single-Walled Carbon Nanotubes Interactions with Mitochondrial Voltage-Dependent Anion Channels Using Molecular Docking and Perturbation Theory. Sci Rep (2017) 0.75
Using chirality to probe the conformational dynamics and assembly of intrinsically disordered amyloid proteins. Sci Rep (2017) 0.75
Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements. Sci Rep (2017) 0.75
Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins (2003) 32.38
Knowledge-based protein secondary structure assignment. Proteins (1995) 14.08
Protein structure prediction using Rosetta. Methods Enzymol (2004) 12.05
Conformation of polypeptides and proteins. Adv Protein Chem (1968) 11.91
PISCES: a protein sequence culling server. Bioinformatics (2003) 11.87
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res (2004) 9.86
The Uppsala Electron-Density Server. Acta Crystallogr D Biol Crystallogr (2004) 9.60
Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci (1997) 7.92
Influence of proline residues on protein conformation. J Mol Biol (1991) 4.87
Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci (2003) 4.82
Protein-protein docking with backbone flexibility. J Mol Biol (2007) 4.32
Rotamer libraries in the 21st century. Curr Opin Struct Biol (2002) 4.09
Modeling structurally variable regions in homologous proteins with rosetta. Proteins (2004) 3.64
Probability plotting methods for the analysis of data. Biometrika (1968) 3.57
PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res (2005) 3.55
The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding. Proc Natl Acad Sci U S A (2000) 3.39
Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J Mol Biol (1987) 3.08
Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci (1996) 2.90
Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys J (2005) 2.84
Beta-turns and their distortions: a proposed new nomenclature. Protein Eng (1990) 2.67
Conformation dependence of backbone geometry in proteins. Structure (2009) 2.33
Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures. Nat Struct Biol (1995) 2.32
Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides. J Mol Biol (2003) 2.00
Conformations of amino acids in proteins. Acta Crystallogr D Biol Crystallogr (2002) 1.95
Loop modeling: Sampling, filtering, and scoring. Proteins (2008) 1.81
Density Estimation for Protein Conformation Angles Using a Bivariate von Mises Distribution and Bayesian Nonparametrics. J Am Stat Assoc (2009) 1.78
Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix. Protein Sci (2003) 1.73
Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry (2005) 1.73
Objectively judging the quality of a protein structure from a Ramachandran plot. Comput Appl Biosci (1997) 1.52
Statistical and conformational analysis of the electron density of protein side chains. Proteins (2007) 1.35
The Ramachandran plots of glycine and pre-proline. BMC Struct Biol (2005) 1.20
Local propensities and statistical potentials of backbone dihedral angles in proteins. J Mol Biol (2004) 1.09
Relationships between amino acid sequence and backbone torsion angle preferences. Proteins (2004) 1.06
Neighbor effect on PPII conformation in alanine peptides. J Am Chem Soc (2005) 1.01
Assessing side-chain perturbations of the protein backbone: a knowledge-based classification of residue Ramachandran space. J Mol Biol (2008) 1.00
Main-chain conformational tendencies of amino acids. Proteins (2005) 0.98
Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities. Proteins (2008) 0.95
Bayesian statistical studies of the Ramachandran distribution. Stat Appl Genet Mol Biol (2005) 0.93
Influence of the local amino acid sequence upon the zones of the torsional angles phi and psi adopted by residues in proteins. Biochemistry (1991) 0.80
Computational basis of knowledge-based conformational probabilities derived from local- and long-range interactions in proteins. Proteins (2007) 0.80
PISCES: a protein sequence culling server. Bioinformatics (2003) 11.87
Optimal feedback control as a theory of motor coordination. Nat Neurosci (2002) 11.57
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
Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci U S A (2004) 5.10
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
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
A statistical framework for genomic data fusion. Bioinformatics (2004) 3.64
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
Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol (2005) 3.14
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
Genomic privacy and limits of individual detection in a pool. Nat Genet (2009) 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
Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet (2005) 2.32
On the inference of ancestries in admixed populations. Genome Res (2008) 2.27
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
Convex and semi-nonnegative matrix factorizations. IEEE Trans Pattern Anal Mach Intell (2010) 1.89
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
A randomization test for controlling population stratification in whole-genome association studies. Am J Hum Genet (2007) 1.73
Scoring profile-to-profile sequence alignments. Protein Sci (2004) 1.71
Sensorimotor adaptation of speech I: Compensation and adaptation. J Speech Lang Hear Res (2002) 1.70
Assessment of disorder predictions in CASP6. Proteins (2005) 1.69
Subtree power analysis and species selection for comparative genomics. Proc Natl Acad Sci U S A (2005) 1.69
Promotion of tumor growth by murine fibroblast activation protein, a serine protease, in an animal model. Cancer Res (2002) 1.66
Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc Natl Acad Sci U S A (2003) 1.60
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
Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics (2004) 1.46
Assessment of fold recognition predictions in CASP6. Proteins (2005) 1.41
MollDE: a homology modeling framework you can click with. Bioinformatics (2005) 1.40
Statistical and conformational analysis of the electron density of protein side chains. Proteins (2007) 1.35
Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses. J Bacteriol (2005) 1.31
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
A dual receptor crosstalk model of G-protein-coupled signal transduction. PLoS Comput Biol (2008) 1.20
Consistent probabilistic outputs for protein function prediction. Genome Biol (2008) 1.17
Logos: a modular bayesian model for de novo motif detection. J Bioinform Comput Biol (2004) 1.16
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
Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res (2011) 1.10
A latent variable model for chemogenomic profiling. Bioinformatics (2005) 1.10
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
Active site prediction using evolutionary and structural information. Bioinformatics (2010) 1.09
Comprehensive next-generation sequence analyses of the entire mitochondrial genome reveal new insights into the molecular diagnosis of mitochondrial DNA disorders. Genet Med (2013) 1.07
Domain definition and target classification for CASP6. Proteins (2005) 1.06
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data. Bioinformatics (2009) 1.06
A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions. Acta Crystallogr D Biol Crystallogr (2008) 1.05
Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase. Proteins (2010) 1.03
Minimal ensembles of side chain conformers for modeling protein-protein interactions. Proteins (2011) 1.03
Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation. Proc Natl Acad Sci U S A (2005) 1.03
Quasi-consensus-based comparison of profile hidden Markov models for protein sequences. Bioinformatics (2005) 1.02
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
Transition to next generation analysis of the whole mitochondrial genome: a summary of molecular defects. Hum Mutat (2013) 0.99
Rapid calcium-dependent activation of Aurora-A kinase. Nat Commun (2010) 0.98
Phylogenetic inference via sequential Monte Carlo. Syst Biol (2012) 0.95
Development of a rotamer library for use in beta-peptide foldamer computational design. J Am Chem Soc (2010) 0.93
Clinical trials that explicitly exclude gay and lesbian patients. N Engl J Med (2010) 0.92
Prediction of phenotypes of missense mutations in human proteins from biological assemblies. Proteins (2012) 0.92
The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite. PLoS One (2013) 0.91
Roles of Tyr122-hydrophobic cluster and K+ binding in Ca2+ -releasing process of ADP-insensitive phosphoenzyme of sarcoplasmic reticulum Ca2+ -ATPase. J Biol Chem (2008) 0.90
Evolutionary inference via the Poisson Indel Process. Proc Natl Acad Sci U S A (2012) 0.89
LOGOS: a modular Bayesian model for de novo motif detection. Proc IEEE Comput Soc Bioinform Conf (2003) 0.88
An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases. Proteins (2009) 0.88
Bayesian haplotype inference via the Dirichlet process. J Comput Biol (2007) 0.87
Architecture and assembly of HIV integrase multimers in the absence of DNA substrates. J Biol Chem (2013) 0.87
Feature space resampling for protein conformational search. Proteins (2010) 0.87
Association mapping and significance estimation via the coalescent. Am J Hum Genet (2008) 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
Identification and characterization of a paralog of human cell cycle checkpoint gene HUS1. Genomics (2002) 0.86
A structural basis for half-of-the-sites metal binding revealed in Drosophila melanogaster porphobilinogen synthase. J Biol Chem (2003) 0.86
An assessment of substitution scores for protein profile-profile comparison. Bioinformatics (2011) 0.85
Learning Low-Dimensional Signal Models: A Bayesian approach based on incomplete measurements. IEEE Signal Process Mag (2011) 0.84
Computational and statistical tradeoffs via convex relaxation. Proc Natl Acad Sci U S A (2013) 0.83
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
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
Phylogenetic molecular function annotation. J Phys Conf Ser (2009) 0.81
Nonparametric combinatorial sequence models. J Comput Biol (2011) 0.80
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
Biochemical, molecular, and clinical diagnoses of patients with cerebral creatine deficiency syndromes. Mol Genet Metab (2013) 0.80
OVCA2 is downregulated and degraded during retinoid-induced apoptosis. Int J Cancer (2002) 0.79
Roles of interaction between actuator and nucleotide binding domains of sarco(endo)plasmic reticulum Ca(2+)-ATPase as revealed by single and swap mutational analyses of serine 186 and glutamate 439. J Biol Chem (2009) 0.79