Published in Science on October 05, 2001
Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc (2009) 32.64
I-TASSER server for protein 3D structure prediction. BMC Bioinformatics (2008) 18.28
TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res (2014) 8.86
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci (2002) 5.47
Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A (2004) 5.44
Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc (2009) 5.42
LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res (2007) 5.30
Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (2010) 5.08
Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol (2007) 5.07
MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2004) 4.54
The protein folding problem. Annu Rev Biophys (2008) 4.43
Critical assessment of methods of protein structure prediction (CASP)--round x. Proteins (2013) 3.78
Template-based protein structure modeling using the RaptorX web server. Nat Protoc (2012) 3.68
Tools for comparative protein structure modeling and analysis. Nucleic Acids Res (2003) 3.68
MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res (2006) 3.56
I-TASSER: fully automated protein structure prediction in CASP8. Proteins (2009) 3.21
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci U S A (2007) 3.15
Protein structure fitting and refinement guided by cryo-EM density. Structure (2008) 3.12
ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2010) 2.96
Statistical potentials for fold assessment. Protein Sci (2002) 2.92
Functional classification using phylogenomic inference. PLoS Comput Biol (2006) 2.88
Alignment of protein sequences by their profiles. Protein Sci (2004) 2.80
The Protein Model Portal--a comprehensive resource for protein structure and model information. Database (Oxford) (2013) 2.76
The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci U S A (2005) 2.75
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA (2009) 2.63
Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res (2003) 2.44
Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput Biol (2006) 2.40
JPred4: a protein secondary structure prediction server. Nucleic Acids Res (2015) 2.37
Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings. Proc Natl Acad Sci U S A (2005) 2.35
Assessing the limits of genomic data integration for predicting protein networks. Genome Res (2005) 2.33
Data to knowledge: how to get meaning from your result. IUCrJ (2015) 2.23
Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov (2009) 2.23
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Natl Acad Sci U S A (2010) 2.22
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J (2004) 2.13
Toward better refinement of comparative models: predicting loops in inexact environments. Proteins (2008) 2.06
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol (2005) 2.04
MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res (2008) 2.02
MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res (2002) 2.01
The Protein Model Portal. J Struct Funct Genomics (2008) 2.01
A composite score for predicting errors in protein structure models. Protein Sci (2006) 1.92
Structural genomics: a pipeline for providing structures for the biologist. Protein Sci (2002) 1.91
The Enzyme Function Initiative. Biochemistry (2011) 1.87
Low-homology protein threading. Bioinformatics (2010) 1.83
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
Protein folding by zipping and assembly. Proc Natl Acad Sci U S A (2007) 1.72
Comparative structural modeling and inference of conserved protein classes in Drosophila seminal fluid. Proc Natl Acad Sci U S A (2004) 1.66
Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci (2004) 1.66
A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes. Biophys J (2009) 1.63
An extended structure of the APOBEC3G catalytic domain suggests a unique holoenzyme model. J Mol Biol (2009) 1.62
High-throughput computational and experimental techniques in structural genomics. Genome Res (2004) 1.55
Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics (2008) 1.54
How well can the accuracy of comparative protein structure models be predicted? Protein Sci (2008) 1.52
A two-stage approach for improved prediction of residue contact maps. BMC Bioinformatics (2006) 1.52
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinformatics (2008) 1.50
ASTRO-FOLD: a combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys J (2003) 1.47
Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions. Protein Sci (2008) 1.45
Computer-aided antibody design. Protein Eng Des Sel (2012) 1.44
Structure-function mapping of a heptameric module in the nuclear pore complex. J Cell Biol (2012) 1.44
Protein structure prediction for the male-specific region of the human Y chromosome. Proc Natl Acad Sci U S A (2004) 1.43
iMolTalk: an interactive, internet-based protein structure analysis server. Nucleic Acids Res (2004) 1.41
Membrane model for the G-protein-coupled receptor rhodopsin: hydrophobic interface and dynamical structure. Biophys J (2004) 1.41
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics (2008) 1.41
Progress towards mapping the universe of protein folds. Genome Biol (2004) 1.41
In silico screening for novel inhibitors of DNA polymerase III alpha subunit of Mycobacterium tuberculosis (MtbDnaE2, H37Rv). PLoS One (2015) 1.41
The significance of G protein-coupled receptor crystallography for drug discovery. Pharmacol Rev (2011) 1.39
Structural Stability, Transitions, and Interactions within SoxYZCD-Thiosulphate from Sulfurimonas denitrificans: An In Silico Molecular Outlook for Maintaining Environmental Sulphur Cycle. J Biophys (2016) 1.38
A comprehensive analysis of 40 blind protein structure predictions. BMC Struct Biol (2002) 1.37
Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proc Natl Acad Sci U S A (2004) 1.36
Molecular docking screens using comparative models of proteins. J Chem Inf Model (2009) 1.36
Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. BMC Bioinformatics (2007) 1.34
QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC Struct Biol (2009) 1.33
An analysis of core deformations in protein superfamilies. Biophys J (2004) 1.33
Ab initio protein structure prediction using chunk-TASSER. Biophys J (2007) 1.32
M4T: a comparative protein structure modeling server. Nucleic Acids Res (2007) 1.32
Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies. Proteins (2009) 1.32
Fold assessment for comparative protein structure modeling. Protein Sci (2007) 1.31
MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics (2010) 1.30
Characterization of proteins with wide-angle X-ray solution scattering (WAXS). J Struct Funct Genomics (2010) 1.30
Alternatively spliced isoforms of the human constitutive androstane receptor. Nucleic Acids Res (2003) 1.30
Solvent dramatically affects protein structure refinement. Proc Natl Acad Sci U S A (2008) 1.29
Comparison of human solute carriers. Protein Sci (2010) 1.29
Application of sparse NMR restraints to large-scale protein structure prediction. Biophys J (2004) 1.28
Pcons.net: protein structure prediction meta server. Nucleic Acids Res (2007) 1.28
Protein fragment reconstruction using various modeling techniques. J Comput Aided Mol Des (2003) 1.26
@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes. Nucleic Acids Res (2009) 1.26
Identification of monomorphic and divergent haplotypes in the 2006-2007 norovirus GII/4 epidemic population by genomewide tracing of evolutionary history. J Virol (2008) 1.26
Practical lessons from protein structure prediction. Nucleic Acids Res (2005) 1.25
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins (2008) 1.25
Protein loop modeling by using fragment assembly and analytical loop closure. Proteins (2010) 1.25
Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci (2009) 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
Protein structure and evolutionary history determine sequence space topology. Genome Res (2005) 1.22
De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PLoS One (2008) 1.20
Protein sequence entropy is closely related to packing density and hydrophobicity. Protein Eng Des Sel (2005) 1.20
Homology modeling of opioid receptor-ligand complexes using experimental constraints. AAPS J (2005) 1.18
Protein model refinement using an optimized physics-based all-atom force field. Proc Natl Acad Sci U S A (2008) 1.18
Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct (2000) 17.81
Modeling of loops in protein structures. Protein Sci (2000) 9.68
Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor. Cell (2000) 5.73
Structural genomics: beyond the human genome project. Nat Genet (1999) 5.58
Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. Cell (2001) 5.01
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci U S A (1998) 4.17
EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics (2001) 3.24
Research priorities. Shining light into black boxes. Science (2012) 3.06
Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell (2001) 2.84
Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem Sci (2000) 2.73
Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci (1992) 2.61
Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc Biol Sci (1990) 2.53
Evaluation of comparative protein structure modeling by MODELLER-3. Proteins (1997) 2.39
Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell (1997) 2.16
Advances in comparative protein-structure modelling. Curr Opin Struct Biol (1997) 2.08
Identification and characterization of a p53 homologue in Drosophila melanogaster. Proc Natl Acad Sci U S A (2000) 2.04
Protein structure modeling for structural genomics. Nat Struct Biol (2000) 1.98
lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS. Neuron (1999) 1.98
Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat Genet (2001) 1.97
Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol Biol (2000) 1.91
Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase. Cell (1998) 1.90
Theoretical studies of protein folding and unfolding. Curr Opin Struct Biol (1995) 1.89
Crystal structures of ribosome anti-association factor IF6. Nat Struct Biol (2000) 1.81
Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk. Structure (1995) 1.76
A phosphoglucomutase-like gene essential for the optimal expression of methicillin resistance in Staphylococcus aureus: molecular cloning and DNA sequencing. Microb Drug Resist (1996) 1.60
DBAli: a database of protein structure alignments. Bioinformatics (2001) 1.60
Ligand specificity of brain lipid-binding protein. J Biol Chem (1996) 1.54
Improving functional annotation of non-synonomous SNPs with information theory. Pac Symp Biocomput (2005) 1.52
A variable gap penalty function and feature weights for protein 3-D structure comparisons. Protein Eng (1992) 1.51
Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proc Natl Acad Sci U S A (2001) 1.46
Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins. Biochem Soc Trans (1993) 1.37
Domain organization of Escherichia coli transcript cleavage factors GreA and GreB. J Biol Chem (1997) 1.36
Filamentous phage assembly: variation on a protein export theme. Gene (1997) 1.34
Differential mechanisms of inorganic pyrophosphate production by plasma cell membrane glycoprotein-1 and B10 in chondrocytes. Arthritis Rheum (1999) 1.32
Functional links between proteins. Nature (1999) 1.31
Ecto-phosphodiesterase/pyrophosphatase of lymphocytes and non-lymphoid cells: structure and function of the PC-1 family. Immunol Rev (1998) 1.31
ModBase: a database of comparative protein structure models. Bioinformatics (1999) 1.25
Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines on mouse mast cell protease 7 regulates its binding to heparin serglycin proteoglycans. J Biol Chem (1995) 1.23
Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases. Protein Sci (1992) 1.20
Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase. Proc Natl Acad Sci U S A (1999) 1.17
MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res (2000) 1.17
X-ray analyses of aspartic proteinases. III Three-dimensional structure of endothiapepsin complexed with a transition-state isostere inhibitor of renin at 1.6 A resolution. J Mol Biol (1990) 1.14
Immunoglobulin motif DNA recognition and heterodimerization of the PEBP2/CBF Runt domain. Nat Struct Biol (1999) 1.13
Foot drop following brain tumors: case reports. Minim Invasive Neurosurg (1998) 1.12
Site-directed mutagenesis of recombinant human beta 2-glycoprotein I identifies a cluster of lysine residues that are critical for phospholipid binding and anti-cardiolipin antibody activity. J Immunol (1996) 1.12
Acute increases in night-time plasma melatonin levels following a period of meditation. Biol Psychol (2000) 1.11
A common 5'-UTR variant in MATE2-K is associated with poor response to metformin. Clin Pharmacol Ther (2011) 1.07
Chenodeoxycholic acid: a review of its pharmacological properties and therapeutic use. Drugs (1981) 1.06
The tryptase, mouse mast cell protease 7, exhibits anticoagulant activity in vivo and in vitro due to its ability to degrade fibrinogen in the presence of the diverse array of protease inhibitors in plasma. J Biol Chem (1997) 1.04
Phylogenetic relationships from three-dimensional protein structures. Methods Enzymol (1990) 1.03
Tinidazole in the prevention of wound infection after elective colorectal surgery. Med J Aust (1979) 1.03
Identification of a new member of the tryptase family of mouse and human mast cell proteases which possesses a novel COOH-terminal hydrophobic extension. J Biol Chem (1999) 1.02
Human tryptase epsilon (PRSS22), a new member of the chromosome 16p13.3 family of human serine proteases expressed in airway epithelial cells. J Biol Chem (2001) 0.99
Characterization of a di-leucine-based signal in the cytoplasmic tail of the nucleotide-pyrophosphatase NPP1 that mediates basolateral targeting but not endocytosis. Mol Biol Cell (2001) 0.98
Regulation and function of mast cell proteases in inflammation. J Clin Immunol (1998) 0.97
A conserved RGD (Arg-Gly-Asp) motif in the transferrin receptor is required for binding to transferrin. Biochem J (1999) 0.97
Mind-body medicine: stress and its impact on overall health and longevity. Ann N Y Acad Sci (2005) 0.96
Outcome analyses in 1072 surgically treated lumbar disc herniations. Minim Invasive Neurosurg (1999) 0.94
Target practice. Nat Struct Biol (2001) 0.93
Bacterial infections in terminally ill hospice patients. J Pain Symptom Manage (2000) 0.92
Subcutaneous emphysema and pneumothorax following endoscopic sphincterotomy. Aust N Z J Surg (1989) 0.92
Mouse mast cell protease 9, a novel member of the chromosome 14 family of serine proteases that is selectively expressed in uterine mast cells. J Biol Chem (1997) 0.91
The effects of multivitamin supplementation on mood and general well-being in healthy young adults. A laboratory and at-home mobile phone assessment. Appetite (2013) 0.90
Formation of enzymatically active, homotypic, and heterotypic tetramers of mouse mast cell tryptases. Dependence on a conserved Trp-rich domain on the surface. J Biol Chem (2000) 0.89
Gallstones at autopsy and cholecystectomy: a comparative study. Aust N Z J Surg (1988) 0.89
SLC classification: an update. Clin Pharmacol Ther (2013) 0.88
The folding mechanism of larger model proteins: role of native structure. Proc Natl Acad Sci U S A (1996) 0.88
Core histones of the amitochondriate protist, Giardia lamblia. Mol Biol Evol (2000) 0.88
Current insights into the "antiphospholipid" syndrome: clinical, immunological, and molecular aspects. Adv Immunol (1998) 0.87
Percutaneous extraction of retained common bile-duct stones via the T-tube track. Aust N Z J Surg (1988) 0.86
The extent of injuries in VFL footballers. Aust Fam Physician (1981) 0.84
Divalent cations stabilize the conformation of plasma cell membrane glycoprotein PC-1 (alkaline phosphodiesterase I). Biochem J (1994) 0.83
Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases. J Biol Chem (2001) 0.83
Gallstones and gall bladder carcinoma. Aust N Z J Surg (2000) 0.82
Single and multiple cholesterol gallstones and the influence of bacteria. Med Hypotheses (2000) 0.82
Structural basis of allotypes of ecto-nucleotide pyrophosphatase/phosphodiesterase (plasma cell membrane glycoprotein PC-1) in the mouse and rat, and analysis of allele-specific xenogeneic antibodies. Eur J Immunogenet (2002) 0.81
Subdural and intraventricular traumatic tension pneumocephalus: case report. Minim Invasive Neurosurg (2000) 0.81
Can we delay aging? The biology and science of aging. Ann N Y Acad Sci (2005) 0.81
Comparisons of the sequences, 3-D structures and mechanisms of pepsin-like and retroviral aspartic proteinases. Adv Exp Med Biol (1991) 0.81
Association between colorectal polyps and skin tags. Lancet (1985) 0.81
The incidence and nature of Australian Rules football injuries. Aust Fam Physician (1986) 0.80
Autophosphorylation of PC-1 (alkaline phosphodiesterase I/nucleotide pyrophosphatase) and analysis of the active site. Eur J Biochem (1995) 0.79
Serotonin, noradrenaline and cognitive function: a preliminary investigation of the acute pharmacodynamic effects of a serotonin versus a serotonin and noradrenaline reuptake inhibitor. Behav Pharmacol (2000) 0.79
Klatskin tumours: a 20 year experience. Aust N Z J Surg (1989) 0.78
Gastroduodenal hormones and bile-secretion studies in the isolated perfused pig liver. Surgery (1972) 0.78
Primary "brown pigment" bile duct stones. HPB Surg (1991) 0.77
Choledochoplasty for cholecystocholedochal fistula (Mirizzi syndrome type II): a case report and literature review. Aust N Z J Surg (1995) 0.77
Gastro-intestinal hormones and bile secretion in the perfused pig liver: the effects of secretin, cholecystokinin and pentagastrin. Aust N Z J Surg (1974) 0.77
Clinical outcomes in terminally ill patients admitted to hospice care: diagnostic and therapeutic interventions. J Palliat Care (2001) 0.77
Do herbs increase the risk of herb-drug interactions for patients with arthritis? Ann Rheum Dis (2005) 0.77
Prediction of the secondary structures of stefins and cystatins, the low-molecular mass protein inhibitors of cysteine proteinases. Biol Chem Hoppe Seyler (1987) 0.76
Bacteria and gallstone nucleation. Aust N Z J Surg (1989) 0.75
Does drinking carrot juice affect cancer of the prostate? Med J Aust (2001) 0.75
Strategic protein target analysis for developing drugs to stop dental caries. Adv Dent Res (2012) 0.75
[Prospective epidemiologic study for the determination of lung cancer risk groups (1975-19940]. Orv Hetil (1997) 0.75
Is coenzyme Q10 helpful for patients with idiopathic cardiomyopathy? Med J Aust (2001) 0.75
Site-directed mutagenesis of recombinant human beta 2-glycoprotein I. Effect of phospholipid binding and anticardiolipin antibody activity. Ann N Y Acad Sci (1997) 0.75
Liver transplantation in the pig. Med J Aust (1970) 0.75
Aluminium hydroxide in bile-salt diarrhoea. Lancet (1977) 0.75