Published in Proteins on January 01, 2007
I-TASSER server for protein 3D structure prediction. BMC Bioinformatics (2008) 18.28
QMEAN server for protein model quality estimation. Nucleic Acids Res (2009) 3.39
Critical assessment of methods of protein structure prediction-Round VII. Proteins (2007) 3.23
MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics (2008) 1.88
Improved model quality assessment using ProQ2. BMC Bioinformatics (2012) 1.70
Assessment of the assessment: evaluation of the model quality estimates in CASP10. Proteins (2013) 1.60
Evaluation of model quality predictions in CASP9. Proteins (2011) 1.43
QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC Struct Biol (2009) 1.33
Applying undertaker cost functions to model quality assessment. Proteins (2009) 1.23
Model quality assessment using distance constraints from alignments. Proteins (2009) 1.12
Protein structure prediction and model quality assessment. Drug Discov Today (2009) 1.07
SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs. BMC Struct Biol (2008) 1.07
Quality assessment of protein model-structures using evolutionary conservation. Bioinformatics (2010) 1.01
MUFOLD-WQA: A new selective consensus method for quality assessment in protein structure prediction. Proteins (2011) 1.01
Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11. Proteins (2015) 0.94
Predicting the accuracy of protein-ligand docking on homology models. J Comput Chem (2011) 0.94
Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection. BMC Struct Biol (2008) 0.92
Critical assessment of methods of protein structure prediction: Progress and new directions in round XI. Proteins (2016) 0.91
The bHLH142 Transcription Factor Coordinates with TDR1 to Modulate the Expression of EAT1 and Regulate Pollen Development in Rice. Plant Cell (2014) 0.87
Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms. PLoS One (2014) 0.86
An iterative self-refining and self-evaluating approach for protein model quality estimation. Protein Sci (2011) 0.83
Computational predictions of the mutant behavior of AraC. J Mol Biol (2010) 0.82
Benchmarking Deep Networks for Predicting Residue-Specific Quality of Individual Protein Models in CASP11. Sci Rep (2016) 0.81
Quality assessment of protein model-structures based on structural and functional similarities. BMC Bioinformatics (2012) 0.80
Applying Undertaker to quality assessment. Proteins (2009) 0.79
QA-RecombineIt: a server for quality assessment and recombination of protein models. Nucleic Acids Res (2013) 0.79
Structural interpretation of protein-protein interaction network. BMC Struct Biol (2010) 0.77
Closing the side-chain gap in protein loop modeling. J Comput Aided Mol Des (2009) 0.77
BeEP Server: Using evolutionary information for quality assessment of protein structure models. Nucleic Acids Res (2013) 0.77
Modeling of Escherichia coli Endonuclease V structure in complex with DNA. J Mol Model (2008) 0.76
Sorting protein decoys by machine-learning-to-rank. Sci Rep (2016) 0.75
Determining protein similarity by comparing hydrophobic core structure. Heliyon (2017) 0.75
NEW MDS AND CLUSTERING BASED ALGORITHMS FOR PROTEIN MODEL QUALITY ASSESSMENT AND SELECTION. Int J Artif Intell Tools (2013) 0.75
Improved estimation of structure predictor quality. BMC Struct Biol (2009) 0.75
A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell (2011) 9.24
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Critical assessment of methods of protein structure prediction (CASP)--round x. Proteins (2013) 3.78
Critical assessment of methods of protein structure prediction-Round VII. Proteins (2007) 3.23
Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (2003) 2.66
Critical assessment of methods of protein structure prediction (CASP)--round 6. Proteins (2005) 2.58
Critical assessment of methods of protein structure prediction - Round VIII. Proteins (2009) 2.25
Protein function annotation by homology-based inference. Genome Biol (2009) 2.20
Critical assessment of methods of protein structure prediction (CASP)--round IX. Proteins (2011) 2.08
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
Remarkably similar antigen receptors among a subset of patients with chronic lymphocytic leukemia. J Clin Invest (2004) 1.94
The PMDB Protein Model Database. Nucleic Acids Res (2006) 1.94
Binding of the hepatitis C virus E2 glycoprotein to CD81 is strain specific and is modulated by a complex interplay between hypervariable regions 1 and 2. J Virol (2003) 1.89
Ten simple rules for developing a short bioinformatics training course. PLoS Comput Biol (2011) 1.84
Assessment of the assessment: evaluation of the model quality estimates in CASP10. Proteins (2013) 1.60
PIGS: automatic prediction of antibody structures. Bioinformatics (2008) 1.59
Evaluating the usefulness of protein structure models for molecular replacement. Bioinformatics (2005) 1.58
Evolution of bacterial and archaeal multicomponent monooxygenases. J Mol Evol (2003) 1.46
Evaluation of disorder predictions in CASP9. Proteins (2011) 1.46
Evaluation of CASP8 model quality predictions. Proteins (2009) 1.44
Evaluation of model quality predictions in CASP9. Proteins (2011) 1.43
Evaluation of residue-residue contact predictions in CASP9. Proteins (2011) 1.26
Assessment of protein disorder region predictions in CASP10. Proteins (2013) 1.25
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics (2008) 1.23
Discovering regulatory binding-site modules using rule-based learning. Genome Res (2005) 1.19
Stereotyped patterns of B-cell receptor in splenic marginal zone lymphoma. Haematologica (2010) 1.17
Relationship between multiple sequence alignments and quality of protein comparative models. Proteins (2005) 1.16
Automatic procedure for using models of proteins in molecular replacement. Proteins (2007) 1.11
Evaluation of residue-residue contact prediction in CASP10. Proteins (2013) 1.10
The prediction of protein function at CASP6. Proteins (2005) 1.08
Structural repertoire of immunoglobulin λ light chains. Proteins (2011) 1.07
The association of heavy and light chain variable domains in antibodies: implications for antigen specificity. FEBS J (2011) 1.05
Mg2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs. RNA (2007) 1.03
A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins. Bioinformatics (2003) 1.03
The betaI/betaIII-tubulin isoforms and their complexes with antimitotic agents. Docking and molecular dynamics studies. FEBS J (2006) 1.02
Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. Bioinformatics (2009) 1.02
A database of immunoglobulins with integrated tools: DIGIT. Nucleic Acids Res (2011) 1.01
Definition and classification of evaluation units for CASP10. Proteins (2013) 0.99
Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures. Proteins (2006) 0.98
FIDEA: a server for the functional interpretation of differential expression analysis. Nucleic Acids Res (2013) 0.98
Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions. Nucleic Acids Res (2006) 0.97
Exploring the cytochrome c folding mechanism: cytochrome c552 from thermus thermophilus folds through an on-pathway intermediate. J Biol Chem (2003) 0.96
An automatic method for identifying surface proteins in bacteria: SLEP. BMC Bioinformatics (2010) 0.96
Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server. Bioinformatics (2013) 0.96
Small molecule inhibitors of histone arginine methyltransferases: homology modeling, molecular docking, binding mode analysis, and biological evaluations. J Med Chem (2007) 0.95
Classification of proteins based on the properties of the ligand-binding site: the case of adenine-binding proteins. Proteins (2002) 0.94
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Res (2010) 0.93
A model of the complex between the PfEMP1 malaria protein and the human ICAM-1 receptor. Proteins (2007) 0.92
Interaction model based on local protein substructures generalizes to the entire structural enzyme-ligand space. J Chem Inf Model (2008) 0.92
Endocytosis of synaptic ADAM10 in neuronal plasticity and Alzheimer's disease. J Clin Invest (2013) 0.91
Ten years of predictions ... and counting. FEBS J (2005) 0.91
Massive screening of copy number population-scale variation in Bos taurus genome. BMC Genomics (2013) 0.90
MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships. Bioinformatics (2013) 0.89
Improving your target-template alignment with MODalign. Bioinformatics (2012) 0.89
A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity. PLoS One (2009) 0.89
Engineering stable cytoplasmic intrabodies with designed specificity. J Mol Biol (2003) 0.89
System for accepting server predictions in CASP6. Proteins (2005) 0.89
Revisiting the prediction of protein function at CASP6. FEBS J (2006) 0.88
Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions. Proteins (2009) 0.88
Igs expressed by chronic lymphocytic leukemia B cells show limited binding-site structure variability. J Immunol (2013) 0.88
Mutation pattern of paired immunoglobulin heavy and light variable domains in chronic lymphocytic leukemia B cells. Mol Med (2011) 0.88
Yeast as a model of human mitochondrial tRNA base substitutions: investigation of the molecular basis of respiratory defects. RNA (2007) 0.87
MAISTAS: a tool for automatic structural evaluation of alternative splicing products. Bioinformatics (2011) 0.87
Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches. Bioinformatics (2006) 0.87
On the mechanism of chloroquine resistance in Plasmodium falciparum. PLoS One (2010) 0.87
Coding potential of the products of alternative splicing in human. Genome Biol (2011) 0.86
Identification and functional characterization of the bile acid transport proteins in non-mammalian ileum and mammalian liver. Proteins (2008) 0.86
The MEPS server for identifying protein conformational epitopes. BMC Bioinformatics (2007) 0.85
Identification of the Schistosoma mansoni molecular target for the antimalarial drug artemether. J Chem Inf Model (2011) 0.85
A structure-guided approach to an orthogonal estrogen-receptor-based gene switch activated by ligands suitable for in vivo studies. J Med Chem (2006) 0.85
Site-directed enzymatic PEGylation of the human granulocyte colony-stimulating factor. FEBS J (2009) 0.84
Modelling and molecular dynamics of the interaction between the E3 ubiquitin ligase Itch and the E2 UbcH7. Biochem Pharmacol (2008) 0.84
Aminoacylation and conformational properties of yeast mitochondrial tRNA mutants with respiratory deficiency. RNA (2005) 0.84
Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract. BMC Evol Biol (2011) 0.84
Inhibition of endothelial cell migration and angiogenesis by a vascular endothelial growth factor receptor-1 derived peptide. Eur J Cancer (2008) 0.83
Investigation of a potential mechanism for the inhibition of SmTGR by Auranofin and its implications for Plasmodium falciparum inhibition. Biochem Biophys Res Commun (2011) 0.83
PICMI: mapping point mutations on genomes. Bioinformatics (2010) 0.83
A proangiogenic peptide derived from vascular endothelial growth factor receptor-1 acts through alpha5beta1 integrin. Blood (2008) 0.83
The MoVIN server for the analysis of protein interaction networks. BMC Bioinformatics (2008) 0.83
The significance of performance ranking in CASP--response to Marti-Renom et al. Structure (2002) 0.83
Analysis of hepatitis C virus hypervariable region 1 sequence from cryoglobulinemic patients and associated controls. J Virol (2007) 0.83
Using local gene expression similarities to discover regulatory binding site modules. BMC Bioinformatics (2006) 0.82
Dissecting the structural determinants of the interaction between the human cytomegalovirus UL18 protein and the CD85j immune receptor. J Immunol (2008) 0.82
An analysis of the Sargasso Sea resource and the consequences for database composition. BMC Bioinformatics (2006) 0.82
Coordinated and reversible reduction of enzymes involved in terminal oxidative metabolism in skeletal muscle mitochondria from a riboflavin-responsive, multiple acyl-CoA dehydrogenase deficiency patient. Electrophoresis (2006) 0.80
The evaluation of protein structure prediction results. Mol Biotechnol (2007) 0.79
A resource for benchmarking the usefulness of protein structure models. BMC Bioinformatics (2012) 0.78
No protein is an island. Curr Opin Struct Biol (2009) 0.78
ProCoCoA: A quantitative approach for analyzing protein core composition. Comput Biol Chem (2012) 0.78
Toward a better understanding of the interaction between TGF-β family members and their ALK receptors. J Mol Model (2012) 0.77
Detecting mutually exclusive interactions in protein-protein interaction maps. PLoS One (2012) 0.75