Published in Bioinformatics on February 04, 2012
Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV). F1000Res (2014) 0.91
MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships. Bioinformatics (2013) 0.89
Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). Bioinformatics (2014) 0.82
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 33.07
Protein homology detection by HMM-HMM comparison. Bioinformatics (2004) 21.92
PyCogent: a toolkit for making sense from sequence. Genome Biol (2007) 20.64
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods (2011) 6.06
SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res (2005) 5.59
Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (2010) 5.08
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome. Nucleic Acids Res (2002) 1.47
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics (2005) 34.83
The SWISS-MODEL Repository and associated resources. Nucleic Acids Res (2008) 11.61
A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell (2011) 9.24
Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc (2009) 5.42
Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (2010) 5.08
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res (2004) 4.30
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
Assessment of CASP7 predictions for template-based modeling targets. Proteins (2007) 3.50
Automated server predictions in CASP7. Proteins (2007) 3.40
QMEAN server for protein model quality estimation. Nucleic Acids Res (2009) 3.39
Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis (2009) 3.25
Critical assessment of methods of protein structure prediction-Round VII. Proteins (2007) 3.23
The SWISS-MODEL Repository: new features and functionalities. Nucleic Acids Res (2006) 3.00
The Protein Model Portal--a comprehensive resource for protein structure and model information. Database (Oxford) (2013) 2.76
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
Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. Genes Dev (2009) 2.44
Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32
Critical assessment of methods of protein structure prediction - Round VIII. Proteins (2009) 2.25
Assessment of predictions in the model quality assessment category. Proteins (2007) 2.25
Protein function annotation by homology-based inference. Genome Biol (2009) 2.20
Assessment of template based protein structure predictions in CASP9. Proteins (2011) 2.14
Critical assessment of methods of protein structure prediction (CASP)--round IX. Proteins (2011) 2.08
The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res (2008) 2.03
The Protein Model Portal. J Struct Funct Genomics (2008) 2.01
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
CASP9 target classification. Proteins (2011) 1.75
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
Assessment of disorder predictions in CASP7. Proteins (2007) 1.51
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics (2013) 1.50
Assessment of ligand-binding residue predictions in CASP9. Proteins (2011) 1.47
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
The plug domain of yeast Sec61p is important for efficient protein translocation, but is not essential for cell viability. Mol Biol Cell (2006) 1.42
Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure (2013) 1.39
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics (2011) 1.36
QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC Struct Biol (2009) 1.33
Evaluation of residue-residue contact predictions in CASP9. Proteins (2011) 1.26
Assessment of protein disorder region predictions in CASP10. Proteins (2013) 1.25
Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins (2009) 1.24
Domain definition and target classification for CASP7. Proteins (2007) 1.23
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics (2008) 1.23
Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Res (2007) 1.22
OpenStructure: a flexible software framework for computational structural biology. Bioinformatics (2010) 1.22
Automated protein structure homology modeling: a progress report. Pharmacogenomics (2004) 1.19
Mutations in the TMPRSS3 gene are a rare cause of childhood nonsyndromic deafness in Caucasian patients. J Mol Med (Berl) (2001) 1.19
Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal. Methods Mol Biol (2012) 1.18
Stereotyped patterns of B-cell receptor in splenic marginal zone lymphoma. Haematologica (2010) 1.17
Mutations in the Sec61p channel affecting signal sequence recognition and membrane protein topology. J Biol Chem (2007) 1.17
Relationship between multiple sequence alignments and quality of protein comparative models. Proteins (2005) 1.16
Novel inhibitors of dengue virus methyltransferase: discovery by in vitro-driven virtual screening on a desktop computer grid. J Med Chem (2010) 1.13
Phylogenetic analysis of haloalkane dehalogenases. Proteins (2007) 1.12
Automatic procedure for using models of proteins in molecular replacement. Proteins (2007) 1.11
The mouse eugenol odorant receptor: structural and functional plasticity of a broadly tuned odorant binding pocket. Biochemistry (2010) 1.10
Evaluation of residue-residue contact prediction in CASP10. Proteins (2013) 1.10
How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding. Proteins (2006) 1.08
The prediction of protein function at CASP6. Proteins (2005) 1.08
Comparison of 68Ga-DOTANOC and 68Ga-DOTATATE PET/CT within patients with gastroenteropancreatic neuroendocrine tumors. J Nucl Med (2013) 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
Asp1424Asn MYH9 mutation results in an unstable protein responsible for the phenotypes in May-Hegglin anomaly/Fechtner syndrome. Blood (2003) 1.04
Mg2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs. RNA (2007) 1.03
The betaI/betaIII-tubulin isoforms and their complexes with antimitotic agents. Docking and molecular dynamics studies. FEBS J (2006) 1.02
A database of immunoglobulins with integrated tools: DIGIT. Nucleic Acids Res (2011) 1.01
Novel cargo-binding site in the beta and delta subunits of coatomer. J Cell Biol (2007) 1.00
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
REPAIRtoire--a database of DNA repair pathways. Nucleic Acids Res (2010) 0.97
Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server. Bioinformatics (2013) 0.96
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
Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein. PLoS One (2007) 0.95
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
Assessment of ligand binding site predictions in CASP10. Proteins (2014) 0.93
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
Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase. Nucleic Acids Res (2006) 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
Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure. Protein Sci (2004) 0.90
Massive screening of copy number population-scale variation in Bos taurus genome. BMC Genomics (2013) 0.90
Sulfonylureas and glinides exhibit peroxisome proliferator-activated receptor gamma activity: a combined virtual screening and biological assay approach. Mol Pharmacol (2006) 0.89
MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships. Bioinformatics (2013) 0.89
Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins (2011) 0.89
Engineering stable cytoplasmic intrabodies with designed specificity. J Mol Biol (2003) 0.89
Identifying an interaction site between MutH and the C-terminal domain of MutL by crosslinking, affinity purification, chemical coding and mass spectrometry. Nucleic Acids Res (2006) 0.89
Mutation pattern of paired immunoglobulin heavy and light variable domains in chronic lymphocytic leukemia B cells. Mol Med (2011) 0.88