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Links tagged with 'protein sequence analysis'

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PfamDatabase Content

http://pfam.sanger.ac.uk/ [open in a new window]

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Protein > Databases

Pfam is a database of protein families and domains. The database uses HMMER3, the latest version of the popular profile hidden Markov model package. Pfam release 24.0 contains 11,912 families.

links directory index: 11859
TitlePublication YearGoogle Scholar Citation Count
The Pfam protein families database.2012212
The Pfam protein families database.20101375
The Pfam protein families database.20081524
Pfam: clans, web tools and services.20061648
The Pfam protein families database.20042639
The Pfam protein families database.20022079
The Pfam protein families database.20001281
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.1999545
Pfam: multiple sequence alignments and HMM-profiles of protein domains.1998556
NAR Database Issue 2010
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tagsalgorithms amino acid sequence amino acid sequence homology animals archaeal genome binding sites caenorhabditis elegans computational biology computer communication networks computer graphics encyclopedias as topic factual databases fungal genome genome genomics humans information storage and retrieval internet macromolecular substances markov chains molecular evolution molecular models molecular sequence data multigene family nucleic acid databases phylogeny protein conformation protein databases protein sequence analysis proteins quality control secondary protein structure sequence alignment software statistics as topic tertiary protein structure user-computer interface

Swiss ModelTool Content

http://www.expasy.ch/swissmod/SWISS-MODEL.html [open in a new window]

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Protein > 3-D Structure Prediction

Automated protein modelling server.

links directory index: 11411
TitlePublication YearGoogle Scholar Citation Count
The SWISS-MODEL Repository: new features and functionalities200681
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling20061560
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models2004229
SWISS-MODEL: An automated protein homology-modeling server20032847
Large scale protein modelling and model repository199726
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling19976668
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acid sequence homology animals artificial intelligence automation chemical models computational biology computer simulation factual databases genome humans molecular models molecular sequence data online systems protein conformation protein databases protein sequence analysis protein structural homology proteins reproducibility of results sequence alignment switzerland systems integration

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/ [open in a new window]

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DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

This content is being maintained by kimmen.

links directory index: 4963
TitlePublication YearGoogle Scholar Citation Count
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis200720
MUSCLE: multiple sequence alignment with high accuracy and high throughput20044855
SATCHMO: sequence alignment and tree construction using hidden Markov models200388
Phylogenetic inference in protein superfamilies: analysis of SH2 domains.19980
NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

T-COFFEETool Content

http://www.tcoffee.org/ [open in a new window]

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The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

links directory index: 4274
TitlePublication YearGoogle Scholar Citation Count
R-Coffee: a web server for accurately aligning noncoding RNA sequences200817
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods200768
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments200615
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee2006137
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee2006137
3DCoffee: combining protein sequences and structures within multiple sequence alignments2004222
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment2004121
Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments2003201
T-Coffee: A novel method for fast and accurate multiple sequence alignment20003173
COFFEE: an objective function for multiple sequence alignments1998183
NAR Web Server Issue 2003NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence databases as topic dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans information storage and retrieval internet messenger rna molecular sequence data nucleic acid conformation phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna rna sequence analysis sensitivity and specificity sequence alignment software untranslated rna user-computer interface

InterProDatabase Content

http://www.ebi.ac.uk/interpro/index.html [open in a new window]

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Protein > Domains and Motifs

Integrated database of commonly used signature databases (e.g. PROSITE, PRINTS, SMART, Pfam, ProDom); text- and sequence-based searches.

links directory index: 3869
TitlePublication YearGoogle Scholar Citation Count
InterPro in 2011: new developments in the family and domain prediction database201211
The InterPro BioMart: federated query and web service access to the InterPro Resource20114
InterPro: the integrative protein signature database2009585
New developments in the InterPro database2007392
InterPro, progress and status in 20052005562
The InterPro Database, 2003 brings increased coverage and new features2003700
InterPro: an integrated documentation resource for protein families, domains and functional sites200299
The InterPro database, an integrated documentation resource for protein families, domains and functional sites2001758
InterPro--an integrated documentation resource for protein families, domains and functional sites2000758
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tagsalgorithms amino acid repetitive sequences animals computational biology factual databases humans information services metabolic networks and pathways post-translational protein processing protein databases protein sequence analysis proteins search engine sequence alignment systems integration tertiary protein structure

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html [open in a new window]

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The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

links directory index: 3841
TitlePublication YearGoogle Scholar Citation Count
MEME SUITE: tools for motif discovery and searching2009174
MEME: discovering and analyzing DNA and protein sequence motifs2006507
Meta-MEME: motif-based hidden Markov models of protein families1997223
An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases199757
The megaprior heuristic for discovering protein sequence patterns199628
ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool199697
The value of prior knowledge in discovering motifs with MEME1995492
Fitting a mixture model by expectation maximization to discover motifs in biopolymers19942263
NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation base sequence binding sites biopolymers computer communication networks databases as topic dna dna sequence analysis evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases internet mammals markov chains molecular models molecular sequence data nucleic acid repetitive sequences protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements user-computer interface

PSORT.orgTool Content

http://www.psort.org/ [open in a new window]

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Protein > Localization and Targeting

PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.

links directory index: 3330
TitlePublication YearGoogle Scholar Citation Count
PSORTdb: a protein subcellular localization database for bacteria2005101
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria2003292
Extensive feature detection of N-terminal protein sorting signals2002414
PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization19991544
Better prediction of protein cellular localization sites with the k nearest neighbors classifier1997395
Expert system for predicting protein localization sites in gram-negative bacteria1991584
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence bacterial outer membrane proteins bacterial proteins bayes theorem binding sites cell membrane computational biology cytoplasm decision trees escherichia coli evaluation studies as topic expert systems factual databases fungal proteins gram-negative bacteria humans lipoproteins membrane proteins molecular sequence data neural networks (computer) protein databases protein precursors protein sequence analysis protein sorting signals proteins reproducibility of results saccharomyces cerevisiae secondary protein structure sequence alignment subcellular fractions

Institute of Enzymology ServersTool Content

http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=30&Itemid=... [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting

A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.

links directory index: 2004
TitlePublication YearGoogle Scholar Citation Count
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates200546
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content2005392
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins2005235
BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes200552
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank2005138
Transmembrane proteins in the Protein Data Bank: identification and classification2004138
Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation200443
SCide: identification of stabilization centers in proteins.20030
Servers for sequence-structure relationship analysis and prediction20035
On filtering false positive transmembrane protein predictions200257
The HMMTOP transmembrane topology prediction server.20010
Principles governing amino acid composition of integral membrane proteins: application to topology prediction1998795
Stabilization centers in proteins: identification, characterization and predictions1997103
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acids binding sites capsid proteins cell line chemical models computational biology computer simulation conserved sequence cysteine database management systems dna methylation dna primers drug stability energy transfer genome genomics humans hydrophobic and hydrophilic interactions kringles lipid bilayers markov chains membrane proteins molecular models molecular sequence data neural networks (computer) oxidation-reduction pliability polymerase chain reaction protein binding protein conformation protein databases protein engineering protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment statistical models structure-activity relationship sulfites temperature tertiary protein structure thermodynamics tissue plasminogen activator

NCBI Human DNA Reference SequenceDatabase Content

http://www.ncbi.nlm.nih.gov/RefSeq/ [open in a new window]

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DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Model Organisms > Mouse and Rat
Model Organisms > Yeast

Downloadable human DNA reference sequence as well as other reference genome sequences.

links directory index: 1916
TitlePublication YearGoogle Scholar Citation Count
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy20128
NCBI Reference Sequences: current status, policy and new initiatives2009217
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins2007943
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins2005748
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tagsamino acid sequence animals base sequence dna sequence analysis exons genetic databases genome genomics humans messenger rna mice national library of medicine (u.s.) nucleic acid databases protein databases protein sequence analysis proteins pseudogenes rats reference standards rna sequence analysis sequence analysis systems integration united states untranslated rna

CASTpTool Content

http://sts.bioengr.uic.edu/castp/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

links directory index: 1616
TitlePublication YearGoogle Scholar Citation Count
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues2006372
CASTp: Computed Atlas of Surface Topography of proteins2003264
Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins1998153
Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape1998226
Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design1998601
NAR Web Server Issue 2003NAR Web Server Issue 2006
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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

RosettaDesignTool Content

http://rosettadesign.med.unc.edu [open in a new window]

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Protein > 3-D Structure Prediction
Protein > Biochemical Features

RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.

links directory index: 1600
TitlePublication YearGoogle Scholar Citation Count
RosettaDesign server for protein design200649
Design of a novel globular protein fold with atomic-level accuracy2003716
A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins2003170
Accurate computer-based design of a new backbone conformation in the second turn of protein L200263
Computer-based redesign of a protein folding pathway2001158
Conversion of monomeric protein L to an obligate dimer by computational protein design200144
Native protein sequences are close to optimal for their structures2000400
NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence amino acid sequence homology bacterial proteins biomolecular nuclear magnetic resonance circular dichroism computational biology computer simulation crystallization dimerization dna-binding proteins guanidine kinetics magnetic resonance spectroscopy molecular models molecular sequence data monte carlo method mutagenesis mutation protein conformation protein databases protein denaturation protein engineering protein folding protein sequence analysis proteins secondary protein structure sequence alignment solubility temperature tertiary protein structure thermodynamics x-ray crystallography

Universal Protein Resource (UniProt)Database Content

http://www.uniprot.org [open in a new window]

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Protein > Databases

Universal Protein Resource (UniProt) maintains a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database.

links directory index: 1408
TitlePublication YearGoogle Scholar Citation Count
Reorganizing the protein space at the Universal Protein Resource (UniProt)201213
Ongoing and future developments at the Universal Protein Resource2011154
The Universal Protein Resource (UniProt) in 2010201053
The Universal Protein Resource (UniProt)20071170
Update on genome completion and annotations: Protein Information Resource200418
NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms amino acid sequence animals computational biology europe fungal genome human genome humans nucleic acid databases protein databases protein isoforms protein sequence analysis proteins proteome proteomics systems integration viral genome

ExPASy Molecular Biology ServerResource Content

http://www.expasy.org/ [open in a new window]

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Education > Directories and Portals
Protein > Do-it-all Tools for Protein

ExPASy is the bioinformatics resource portal for access to programs and databases for the analysis of proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.

links directory index: 1342
TitlePublication YearGoogle Scholar Citation Count
ExPASy: The proteomics server for in-depth protein knowledge and analysis20031342
NAR Web Server Issue 2003NAR Web Server Issue 2012
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tagsenzymes gel electrophoresis internet molecular models protein conformation protein databases protein sequence analysis proteins proteomics software systems integration user-computer interface

ProtTestTool Content

http://darwin.uvigo.es/software/prottest_server.html [open in a new window]

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Protein > Phylogeny Reconstruction

ProtTest is a program that determines the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment.

links directory index: 1077
TitlePublication YearGoogle Scholar Citation Count
ProtTest: selection of best-fit models of protein evolution20051077
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tagsalgorithms amino acid sequence amino acid substitution amino acids computer simulation dna mutational analysis genetic models humans molecular evolution molecular models molecular sequence data phylogeny protein sequence analysis proteins site-directed mutagenesis structure-activity relationship

Services from Zhou LaboratoryResource Content

http://cssb.biology.gatech.edu/skolnick/people/zhou.html [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Networks & Interactions, Pathways and Enzymes

Tools from the Zhou laboratory including predictors of transmembrane topology (THUMBUP, UMDHMM-TMHP, TUPS); prediction/analysis tools for tertiary structure (SPARKS2, SP3); and, prediction/analysis tools for interactions (DMONOMER, DLOOP, DMUTANT, DCOMPLEX, DDNA, TCD, DOGMA).

links directory index: 1058
TitlePublication YearGoogle Scholar Citation Count
Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations200520
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments2005136
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential200473
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition2004135
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding200492
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method200360
Folding rate prediction using total contact distance2002139
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction2002403
NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids antigen-antibody complex binding sites biological evolution chemical models computational biology dimerization factual databases hydrogen bonding kinetics markov chains mathematics membrane proteins molecular evolution molecular structure peptide fragments peptide library plant proteins probability protein binding protein conformation protein databases protein folding protein sequence analysis proteins regression analysis reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical models statistics as topic tertiary protein structure theoretical models thermodynamics time factors

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