> Tag > Links tagged with 'amino acid sequence homology'

Links tagged with 'amino acid sequence homology'

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Found 78 links

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SAM-T08Tool Content

http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html [open in a new window]

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Protein > 3-D Structure Prediction
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

The SAM-T08 web server is a 3D protein structure prediction server. The server also provides 3 multiple sequence alignments of putative homologs, prediction of local structural features including backbone and burial properties and residue-residue contact predictions.

links directory index: 40
TitlePublication YearGoogle Scholar Citation Count
SAM-T08, HMM-based protein structure prediction200940
NAR Web Server Issue 2009
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tagsamino acid sequence homology biomolecular nuclear magnetic resonance markov chains molecular models protein conformation protein databases protein structural homology proteins reproducibility of results sequence alignment

ScanPrositeTool Content

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

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Protein > Domains and Motifs

ScanProsite is a tool for detecting PROSITE signature matches in protein sequences. Users can also search protein databases for specific motifs.

This content is being maintained by PROSITE.

links directory index: 612
TitlePublication YearGoogle Scholar Citation Count
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins2006261
ScanProsite: a reference implementation of a PROSITE scanning tool2002351
NAR Web Server Issue 2006
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tagsamino acid sequence homology amino acids computational biology gene expression profiling protein databases protein sequence analysis proteins sequence alignment tertiary protein structure

SCOPDatabase Content

http://scop.mrc-lmb.cam.ac.uk/scop/ [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Databases
Protein > Domains and Motifs

Structural Classification of Proteins - database created by a combination of manual inspection and automated methods. Comprehensive ordering of all proteins of known structure, according to evolutionary and structural relationships.

links directory index: 5646
TitlePublication YearGoogle Scholar Citation Count
SCOP database in 2002: refinements accommodate structural genomics2002476
SCOP: a structural classification of proteins database for the investigation of sequences and structures19955170
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tagsalgorithms amino acid sequence amino acid sequence homology animals antibodies capsid proteins computational biology factual databases genome genomics humans information storage and retrieval internet molecular evolution protein conformation protein databases protein folding protein kinases proteins secondary protein structure sequence alignment sequence analysis statistics as topic tertiary protein structure

SDPpredTool Content

http://bioinf.fbb.msu.ru/SDPpred/ [open in a new window]

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Protein > Annotation and Function
Sequence Comparison > Analysis of Aligned Sequences

SDPpred is a tool for predicting which residues of a protein determine functional differences relative to its homologues. It takes as input an multiple sequence alignment of a protein family divided into groups based on the perceived functional differences.

This content is being maintained by okalinina.

links directory index: 59
TitlePublication YearGoogle Scholar Citation Count
SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins200459
NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence homology amino acids molecular models protein sequence analysis proteins sequence alignment

SEARCHPKSTool Content

http://www.nii.res.in/searchpks.html [open in a new window]

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Protein > Domains and Motifs

SEARCHPKS is a program for the detection and analysis of Polyketide Synthase (PKS) domains.

links directory index: 75
TitlePublication YearGoogle Scholar Citation Count
SEARCHPKS: A program for detection and analysis of polyketide synthase domains200375
NAR Web Server Issue 2003
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tagsamino acid sequence homology molecular models multienzyme complexes protein sequence analysis substrate specificity tertiary protein structure

SelectomeDatabase Content

http://selectome.unil.ch/ [open in a new window]

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Protein > Databases
Protein > Sequence Features
Sequence Comparison > Analysis of Aligned Sequences

Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment.

This content is being maintained by selectome.

links directory index: 53
TitlePublication YearGoogle Scholar Citation Count
Phylogenetic code in the cloud - can it meet the expectations?20102
Selectome: a database of positive selection200913
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes200838
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tagsamino acid sequence homology animals codon computational biology computing methodologies gene duplication genes genetic databases genetic selection medical informatics applications phylogeny proteins software design vertebrates

Sequence HarmonyTool Content

http://www.ibi.vu.nl/programs/seqharmwww/ [open in a new window]

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Protein > Annotation and Function
Sequence Comparison > Analysis of Aligned Sequences

Sequence Harmony detects subfamily specific functional sites from a multiple sequence alignment by scoring compositional differences between given subfamily groupings.

links directory index: 58
TitlePublication YearGoogle Scholar Citation Count
Sequence harmony: detecting functional specificity from alignments200719
Sequence comparison by sequence harmony identifies subtype-specific functional sites200639
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites computational biology conserved sequence entropy membrane transport proteins molecular models molecular sequence data protein sequence analysis proteins ras proteins secondary protein structure sequence alignment smad proteins

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

SGDDatabase Content

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

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Model Organisms > Databases

The Saccharomyces Genome Database (SGD) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae. The information in SGD includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary literature from which these data are derived. Phenotypes and genetic interaction data are also annotated and displayed in SGD.

This content is being maintained by yeastgenome.

links directory index: 1012
TitlePublication YearGoogle Scholar Citation Count
Saccharomyces Genome Database: the genomics resource of budding yeast20127
Saccharomyces Genome Database provides mutant phenotype data201060
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms2004248
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins200362
Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure199946
SGD: Saccharomyces Genome Database1998589
NAR Database Issue 2010
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tagsamino acid motifs amino acid sequence amino acid sequence homology animals base sequence bibliographic databases computational biology factual databases fungal dna fungal genes fungal genome fungal proteins genetic databases humans information storage and retrieval internet molecular models molecular sequence data molecular weight mutation nucleic acid databases nucleic acid sequence homology phenotype protein conformation protein databases saccharomyces cerevisiae saccharomyces cerevisiae proteins saccharomycetales sequence alignment sequence homology software terminology as topic tertiary protein structure

SLiMDiscTool Content

http://bioware.ucd.ie/~slimdisc/ [open in a new window]

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Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Networks & Interactions, Pathways and Enzymes

SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.

links directory index: 74
TitlePublication YearGoogle Scholar Citation Count
The SLiMDisc server: short, linear motif discovery in proteins200724
SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent200650
NAR Web Server Issue 2007
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tagsamino acid motifs amino acid sequence amino acid sequence homology animals biological models computational biology computer simulation humans molecular evolution molecular sequence data protein sequence analysis proteins rats

STING MilleniumTool Content

http://luna.bioc.columbia.edu/SMS/STINGm/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

links directory index: 168
TitlePublication YearGoogle Scholar Citation Count
The Diamond STING server200522
STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database200516
STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces200415
Defining 3D residue environment in protein structures using SCORPION and FORMIGA20043
ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure200415
STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes200422
JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure200422
STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence200344
Analysis of structural and physico-chemical parameters involved in the specificity of binding between alpha-amylases and their inhibitors20009
NAR Web Server Issue 2003NAR Web Server Issue 2005
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tagsacid anhydride hydrolases algorithms alpha-amylases amino acid sequence amino acid sequence homology amino acids animals beetles binding sites chemical models chymotrypsin color computational biology computer simulation conserved sequence enzyme inhibitors fabaceae hiv integrase hydrogen bonding lectins medicinal plants molecular cloning molecular models molecular sequence data molecular structure online systems ovomucin plant lectins plant proteins proprotein convertases protein binding protein conformation protein databases protein interaction mapping protein sequence analysis protein structural homology proteins quaternary protein structure recombinant proteins sequence alignment structure-activity relationship systems integration x-ray crystallography

STRINGDatabase Content

http://string.embl.de/ [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a protein-protein interaction/association database. Both known and predicted interactions are included. The interactions are derived from existing data sources and literature and from high-throughput experiments. Predictions are also made based on an analysis of genomic context.

links directory index: 583
TitlePublication YearGoogle Scholar Citation Count
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored2011172
STRING: known and predicted protein-protein associations, integrated and transferred across organisms2005411
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tagsalgorithms amino acid sequence homology animals artificial gene fusion bacterial genes chromosome mapping computer graphics genome genomics information storage and retrieval internet macromolecular substances multiprotein complexes mycoplasma operon protein databases protein interaction mapping proteins software substrate specificity systems integration trna methyltransferases user-computer interface

SVM-PROTTool Content

http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi [open in a new window]

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Protein > Domains and Motifs
Protein > Sequence Features

Support Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families.

links directory index: 246
TitlePublication YearGoogle Scholar Citation Count
SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence2003246
NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology protein sequence analysis proteins

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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external linksLink on Twitter Link on Wikipedia
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

SYFPEITHIDatabase Content

http://www.syfpeithi.de/ [open in a new window]

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Protein > Databases

SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. The database can be used to predict the immunogenicity of given peptide sequences.

links directory index: 1525
TitlePublication YearGoogle Scholar Citation Count
SYFPEITHI: database for MHC ligands and peptide motifs19991525
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tagsamino acid motifs amino acid sequence amino acid sequence homology animals factual databases humans immunogenicity prediciton ligands major histocompatibility complex molecular sequence data

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