Published in Proteins on December 01, 1993
Modeling of loops in protein structures. Protein Sci (2000) 9.68
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res (2007) 9.16
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Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci (2002) 7.40
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Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
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Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation. J Biomol NMR (1999) 1.96
The PMDB Protein Model Database. Nucleic Acids Res (2006) 1.94
A composite score for predicting errors in protein structure models. Protein Sci (2006) 1.92
MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics (2008) 1.88
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci (2004) 1.74
Functional and structural conservation of CBS domains from CLC chloride channels. J Physiol (2004) 1.67
Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop. EMBO J (2002) 1.66
Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput Biol (2006) 1.65
Benchmarking consensus model quality assessment for protein fold recognition. BMC Bioinformatics (2007) 1.63
Ssu72 is a phosphatase essential for transcription termination of snoRNAs and specific mRNAs in yeast. EMBO J (2003) 1.59
Dynamic force spectroscopy of parallel individual Mucin1-antibody bonds. Proc Natl Acad Sci U S A (2005) 1.58
Domain architecture of the catalytic subunit in the ISW2-nucleosome complex. Mol Cell Biol (2007) 1.57
Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci (2008) 1.56
Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics (2008) 1.54
COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res (2004) 1.53
How well can the accuracy of comparative protein structure models be predicted? Protein Sci (2008) 1.52
Functional characterization of Ape1 variants identified in the human population. Nucleic Acids Res (2000) 1.50
Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation. Proc Natl Acad Sci U S A (2008) 1.50
Crystal structure of the phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with myo-inositol. EMBO J (1995) 1.49
The functional roles of the His247 and His281 residues in folate and proton translocation mediated by the human proton-coupled folate transporter SLC46A1. J Biol Chem (2009) 1.47
Bacillus subtilis YhaM, a member of a new family of 3'-to-5' exonucleases in gram-positive bacteria. J Bacteriol (2002) 1.46
Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins (2009) 1.44
Evaluation of model quality predictions in CASP9. Proteins (2011) 1.43
Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis. Biochemistry (2007) 1.41
Recognition of ERK MAP kinase by PEA-15 reveals a common docking site within the death domain and death effector domain. EMBO J (2002) 1.40
Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human. BMC Genomics (2016) 1.39
Structural and functional similarity of amphibian constitutive androstane receptor with mammalian pregnane X receptor. PLoS One (2014) 1.39
QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC Struct Biol (2009) 1.33
Developmentally regulated expression, alternative splicing and distinct sub-groupings in members of the Schistosoma mansoni venom allergen-like (SmVAL) gene family. BMC Genomics (2008) 1.32
M4T: a comparative protein structure modeling server. Nucleic Acids Res (2007) 1.32
Fold assessment for comparative protein structure modeling. Protein Sci (2007) 1.31
Assessment of template-based protein structure predictions in CASP10. Proteins (2014) 1.29
The PYRIN domain: a member of the death domain-fold superfamily. Protein Sci (2001) 1.29
Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor. Biophys J (2007) 1.28
A cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus is actually a broad specificity phosphatase. Protein Sci (2001) 1.27
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins (2008) 1.25
Molecular dissection of interactions between Rad51 and members of the recombination-repair group. Mol Cell Biol (2001) 1.24
Structural genomics: computational methods for structure analysis. Protein Sci (2003) 1.24
Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis. Biochemistry (2009) 1.23
A biochemical mechanism for the oncogenic potential of the p110beta catalytic subunit of phosphoinositide 3-kinase. Proc Natl Acad Sci U S A (2010) 1.23
Constraint-based, homology model of the extracellular domain of the epithelial Na+ channel α subunit reveals a mechanism of channel activation by proteases. J Biol Chem (2010) 1.23
Blind testing of routine, fully automated determination of protein structures from NMR data. Structure (2012) 1.23
Organic anion transporting polypeptides of the OATP/SLCO superfamily: identification of new members in nonmammalian species, comparative modeling and a potential transport mode. J Membr Biol (2006) 1.23
Rigorous performance evaluation in protein structure modelling and implications for computational biology. Philos Trans R Soc Lond B Biol Sci (2006) 1.22
MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res (2000) 1.17
Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase. Proc Natl Acad Sci U S A (1999) 1.17
Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs. Nucleic Acids Res (2010) 1.16
Discriminating compact nonnative structures from the native structure of globular proteins. Proc Natl Acad Sci U S A (1995) 1.15
Discriminative learning for protein conformation sampling. Proteins (2008) 1.15
Molecular modeling of the von Willebrand factor A2 Domain and the effects of associated type 2A von Willebrand disease mutations. J Mol Model (2004) 1.15
Domain mapping of the Rad51 paralog protein complexes. Nucleic Acids Res (2004) 1.14
The ModFOLD4 server for the quality assessment of 3D protein models. Nucleic Acids Res (2013) 1.13
Six new candidate members of the alpha/beta twisted open-sheet family detected by sequence similarity to flavodoxin. Protein Sci (1994) 1.12
The Drosophila Bruno paralogue Bru-3 specifically binds the EDEN translational repression element. Nucleic Acids Res (2004) 1.11
mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships. BMC Bioinformatics (2001) 1.09
Sequence permutations in the molecular evolution of DNA methyltransferases. BMC Evol Biol (2002) 1.09
Boron toxicity tolerance in barley through reduced expression of the multifunctional aquaporin HvNIP2;1. Plant Physiol (2010) 1.09
DNA sequence-dependent folding determines the divergence in binding specificities between Maf and other bZIP proteins. EMBO J (2001) 1.09
Molecular modeling of the membrane targeting of phospholipase C pleckstrin homology domains. Protein Sci (2003) 1.08
Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density. PLoS Comput Biol (2006) 1.08
New statistical potential for quality assessment of protein models and a survey of energy functions. BMC Bioinformatics (2010) 1.08
Essential roles for imuA'- and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A (2010) 1.07
The dependence of all-atom statistical potentials on structural training database. Biophys J (2004) 1.06
Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains. Proc Natl Acad Sci U S A (2007) 1.06
The reducible complexity of a mitochondrial molecular machine. Proc Natl Acad Sci U S A (2009) 1.05
Exchanging murine and human immunoglobulin constant chains affects the kinetics and thermodynamics of antigen binding and chimeric antibody autoreactivity. PLoS One (2007) 1.05
Functional clustering of mutations in the dimer interface of the nucleotide binding folds of the sulfonylurea receptor. J Biol Chem (2008) 1.03
Molecular mechanism of thioredoxin regulation in photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase. Proc Natl Acad Sci U S A (2007) 1.03
Homozygous FOXE3 mutations cause non-syndromic, bilateral, total sclerocornea, aphakia, microphthalmia and optic disc coloboma. Mol Vis (2010) 1.03
High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases. Protein Sci (2005) 1.03
Structural and functional characterizations reveal the importance of a zinc binding domain in Bloom's syndrome helicase. Nucleic Acids Res (2005) 1.02
RPF: a quality assessment tool for protein NMR structures. Nucleic Acids Res (2012) 1.02
SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines. BMC Bioinformatics (2014) 1.02
A unified model of the GABA(A) receptor comprising agonist and benzodiazepine binding sites. PLoS One (2013) 1.02
qPIPSA: relating enzymatic kinetic parameters and interaction fields. BMC Bioinformatics (2007) 1.01
Structure and function relationship of the autotransport and proteolytic activity of EspP from Shiga toxin-producing Escherichia coli. PLoS One (2009) 1.01
The structure of full-length LysR-type transcriptional regulators. Modeling of the full-length OxyR transcription factor dimer. Nucleic Acids Res (2003) 1.01
Local quality assessment in homology models using statistical potentials and support vector machines. Protein Sci (2007) 1.00
Knowledge-based potentials for proteins. Curr Opin Struct Biol (1995) 3.94
Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput Aided Mol Des (1993) 3.06
Helmholtz free energy of peptide hydrogen bonds in proteins. J Mol Biol (1996) 0.86