Protein secondary structure prediction based on position-specific scoring matrices.

PubWeight™: 33.07‹?› | Rank: Top 0.01% | All-Time Top 10000

🔗 View Article (PMID 10493868)

Published in J Mol Biol on September 17, 1999


D T Jones1

Author Affiliations

1: Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom.

Articles citing this

(truncated to the top 100)

I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66

The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res (2005) 21.68

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR (2009) 16.09

The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32

ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res (2005) 11.90

The PredictProtein server. Nucleic Acids Res (2004) 10.89

Statistical potential for assessment and prediction of protein structures. Protein Sci (2006) 8.98

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res (2014) 8.86

A tissue-specific atlas of mouse protein phosphorylation and expression. Cell (2010) 8.65

The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc (2015) 8.53

Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res (2004) 7.39

PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res (2008) 7.16

Protein structure prediction servers at University College London. Nucleic Acids Res (2005) 6.70

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods (2011) 6.06

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

Histone recognition and large-scale structural analysis of the human bromodomain family. Cell (2012) 5.15

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

TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J (2003) 4.62

The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Genome Biol (2001) 4.39

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature (2012) 4.27

GeneSilico protein structure prediction meta-server. Nucleic Acids Res (2003) 3.98

Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell (2002) 3.91

Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol (2006) 3.86

Protein annotation and modelling servers at University College London. Nucleic Acids Res (2010) 3.77

Can correct protein models be identified? Protein Sci (2003) 3.74

Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics (2006) 3.70

Reversal of DNA alkylation damage by two human dioxygenases. Proc Natl Acad Sci U S A (2002) 3.62

SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res (2000) 3.56

Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biol (2006) 3.45

The MPI Bioinformatics Toolkit for protein sequence analysis. Nucleic Acids Res (2006) 3.45

QMEAN server for protein model quality estimation. Nucleic Acids Res (2009) 3.39

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins (2008) 3.38

Widespread protein aggregation as an inherent part of aging in C. elegans. PLoS Biol (2010) 3.36

Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res (2003) 3.35

Non-classical protein secretion in bacteria. BMC Microbiol (2005) 3.17

Structure-based predictions of Rad1, Rad9, Hus1 and Rad17 participation in sliding clamp and clamp-loading complexes. Nucleic Acids Res (2000) 3.16

PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res (2005) 3.15

The lipodystrophy protein seipin is found at endoplasmic reticulum lipid droplet junctions and is important for droplet morphology. Proc Natl Acad Sci U S A (2007) 3.11

Intrinsic disorder in transcription factors. Biochemistry (2006) 3.06

Adenovirus protein VI mediates membrane disruption following capsid disassembly. J Virol (2005) 3.04

Cascaded multiple classifiers for secondary structure prediction. Protein Sci (2000) 2.97

Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol (2005) 2.94

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins (2012) 2.94

Statistical potentials for fold assessment. Protein Sci (2002) 2.92

Multipass membrane protein structure prediction using Rosetta. Proteins (2006) 2.79

Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol Cell (2012) 2.77

The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci U S A (2005) 2.75

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR (2013) 2.75

The PredictProtein server. Nucleic Acids Res (2003) 2.72

Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins (2005) 2.72

Search and discovery strategies for biotechnology: the paradigm shift. Microbiol Mol Biol Rev (2000) 2.64

PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res (2007) 2.59

Structural framework for DNA translocation via the viral portal protein. EMBO J (2007) 2.58

Toward rational protein crystallization: A Web server for the design of crystallizable protein variants. Protein Sci (2007) 2.57

Structural basis for leucine-rich nuclear export signal recognition by CRM1. Nature (2009) 2.56

Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Mol Cell (2012) 2.54

PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics (2005) 2.51

EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res (2003) 2.50

3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res (2004) 2.50

Structure of the TRPA1 ion channel suggests regulatory mechanisms. Nature (2015) 2.47

Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics (2013) 2.43

Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput Biol (2006) 2.40

Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci (2006) 2.39

Evolution of human calicivirus RNA in vivo: accumulation of mutations in the protruding P2 domain of the capsid leads to structural changes and possibly a new phenotype. J Virol (2003) 2.37

Protein flexibility and intrinsic disorder. Protein Sci (2004) 2.33

Substrate specificity of gamma-secretase and other intramembrane proteases. Cell Mol Life Sci (2008) 2.29

Transmembrane helix predictions revisited. Protein Sci (2002) 2.28

piggyBac can bypass DNA synthesis during cut and paste transposition. EMBO J (2008) 2.27

Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses. Proc Natl Acad Sci U S A (2005) 2.26

The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nat Struct Mol Biol (2008) 2.26

The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing. EMBO J (2010) 2.25

Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix. Mol Microbiol (2010) 2.24

Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. PLoS One (2007) 2.22

Nuclear import by karyopherin-βs: recognition and inhibition. Biochim Biophys Acta (2010) 2.19

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics (2011) 2.13

Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J (2004) 2.13

Human PrimPol mutation associated with high myopia has a DNA replication defect. Nucleic Acids Res (2014) 2.12

Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Nucleic Acids Res (2009) 2.09

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics (2008) 2.08

Metazoan Scc4 homologs link sister chromatid cohesion to cell and axon migration guidance. PLoS Biol (2006) 2.08

High-throughput production of human proteins for crystallization: the SGC experience. J Struct Biol (2010) 2.07

Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Nat Struct Mol Biol (2008) 2.07

Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins. Nature (2012) 2.03

Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse. Mol Cell Proteomics (2012) 2.03

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proc Natl Acad Sci U S A (2012) 2.02

Roles of pgaABCD genes in synthesis, modification, and export of the Escherichia coli biofilm adhesin poly-beta-1,6-N-acetyl-D-glucosamine. J Bacteriol (2008) 2.02

PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Res (2014) 2.00

DiANNA: a web server for disulfide connectivity prediction. Nucleic Acids Res (2005) 1.98

AlgK is a TPR-containing protein and the periplasmic component of a novel exopolysaccharide secretin. Structure (2010) 1.97

Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res (2006) 1.96

Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res (2005) 1.95

The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Proc Natl Acad Sci U S A (2004) 1.93

Glycosylation site prediction using ensembles of Support Vector Machine classifiers. BMC Bioinformatics (2007) 1.93

A composite score for predicting errors in protein structure models. Protein Sci (2006) 1.92

Mutations in the KIAA0196 gene at the SPG8 locus cause hereditary spastic paraplegia. Am J Hum Genet (2006) 1.92

Identification and expression of human cytomegalovirus transcription units coding for two distinct Fcgamma receptor homologs. J Virol (2002) 1.92

CASP9 assessment of free modeling target predictions. Proteins (2011) 1.90