> Tag > Links tagged with 'amino acid sequence'

Links tagged with 'amino acid sequence'

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Found 129 links

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BTEVALTool Content

http://www.imtech.res.in/raghava/bteval [open in a new window]

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The aim of BTEVAL server is to evaluate beta turn prediction algorithms on a uniform data set of 426 proteins or subsets of these proteins. It is the new data set in which no two protein chains have more that 25% sequence identity and each chain contains minimum one beta turn.

This content is being maintained by raghavagps.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
BTEVAL: a server for evaluation of beta-turn prediction methods20033
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tagsalgorithms amino acid sequence beta-turn btpred chou-fasman computational biology computer simulation gorbturn molecular models molecular sequence data prediction protein protein databases proteins secondary protein structure thornton

Cascade PSI-BlastDatabase Content

http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html [open in a new window]

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Protein > Domains and Motifs
Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching and Classification

Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains20068
Assessment of a rigorous transitive profile based search method to detect remotely similar proteins200510
NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology molecular models molecular sequence data protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment tertiary protein structure

CDDDatabase Content

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

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Protein > Databases

NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships.

This content is being maintained by Aron Marchler-Bauer.

links directory index: 208
TitlePublication YearGoogle Scholar Citation Count
CDD: a Conserved Domain Database for the functional annotation of proteins2011208
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsamino acid sequence biological models conserved sequence protein databases protein sequence analysis proteins tertiary protein structure

CE-MCTool Content

http://bioinformatics.albany.edu/~cemc/ [open in a new window]

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

A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.

links directory index: 146
TitlePublication YearGoogle Scholar Citation Count
CE-MC: a multiple protein structure alignment server200481
A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization200165
NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence amino acid sequence homology aspartic acid endopeptidases factual databases molecular sequence data monte carlo method protein kinases proteins secondary protein structure sequence alignment software design

CHpredictTool Content

http://www.imtech.res.in/raghava/chpredict [open in a new window]

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Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes

The CHpredict server predict two types of interactions: C-H...O and C-H...π interactions. For C-H...O interaction, the server predicts the residues whose backbone Cα atoms are involved in interaction with backbone oxygen atoms and for C-H...π interactions, it predicts the residues whose backbone Cα atoms are involved in interaction with π ring system of side chain aromatic moieties.

This content is being maintained by raghavagps.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Prediction of C alpha-H...O and C alpha-H...pi interactions in proteins using recurrent neural network20063
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tagsalgorithms alpha H O amino acid sequence ANN C alpha H pi computer simulation hydrogen bonding hydrogen bonding interactions molecular models molecular sequence data neural networks (computer) protein databases protein sequence analysis proteins secondary protein structure weak interactions

CIPRO 2.5Database Content

http://cipro.ibio.jp/2.5 [open in a new window]

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Model Organisms > Databases

The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The CIPRO database collects published data as well as unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data. Homologs in humans and major model organisms are included. Annotations are open to evaluation by users through the CIPRO website.

This content is being maintained by tendo.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality20116
NAR Database Issue 2011
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tagsamino acid sequence animals ciona intestinalis computational biology gene expression profiling genomics molecular sequence annotation protein databases proteome proteomics systems integration

ClotbaseDatabase Content

http://www.clotbase.bicnirrh.res.in/ [open in a new window]

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Protein > Databases

ClotBase is a curated knowledgebase on the proteins that are involved in the blood coagulation pathway. It contains information on sequence, accession number, source, taxonomy, keywords, function, subcellular location, tissue specificity, associated diseases , mutation and links to external databases

links directory index: 0
TitlePublication YearGoogle Scholar Citation Count
ClotBase: a knowledgebase on proteins involved in blood coagulation.20100
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tagsamino acid sequence animals blood coagulation blood coagulation disorders blood coagulation factors blood proteins consensus sequence factual databases genetic databases humans molecular sequence data mutation mutation prediction mutations protein conformation protein databases proteins sequence alignment

CMATool Content

http://www.gene-regulation.com/pub/programs/cma/CMA.html [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.

links directory index: 66
TitlePublication YearGoogle Scholar Citation Count
Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm200623
Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations200643
NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence binding sites chemical models computer simulation dna sequence analysis endothelial cells gene expression profiling genetic promoter regions humans molecular sequence data protein binding protein sequence analysis transcription factors

COGsTool Content

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

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Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

links directory index: 3211
TitlePublication YearGoogle Scholar Citation Count
The COG database: new developments in phylogenetic classification of proteins from complete genomes20011177
A genomic perspective on protein families19972034
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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

Combinatorial Extension of the Optimal PathDatabase Content

http://cl.sdsc.edu/ce.html [open in a new window]

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Protein > 3-D Structure Comparison

Calculates structural alignments between two protein chains; or between a single chain and the entire Protein Data Bank.

links directory index: 1542
TitlePublication YearGoogle Scholar Citation Count
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path19981542
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tagsalgorithms amino acid sequence amino acid sequence homology molecular sequence data monte carlo method protein conformation protein folding proteins sequence alignment

CRPDatabase Content

http://fasta.bioch.virginia.edu/crp/ [open in a new window]

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Protein > Domains and Motifs
Protein > Sequence Features

Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
CRP: Cleavage of Radiolabeled Phosphoproteins20039
A strategy for the rapid identification of phosphorylation sites in the phosphoproteome200240
NAR Web Server Issue 2003
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tagsamino acid sequence biochemistry dna sequence analysis humans molecular sequence data neoplasm proteins neural networks (computer) phosphoproteins phosphorylation phosphoserine phosphothreonine phosphotyrosine protein sequence analysis proteins radioactive tracers recombinant proteins sensitivity and specificity

DATFDatabase Content

http://datf.cbi.pku.edu.cn [open in a new window]

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Expression > Gene Regulation
Model Organisms > Plants

The Database of Arabidopsis Transcription Factors (DATF) contains information of more than 1800 known and predicted transcription factors for Arabidopsis.

links directory index: 164
TitlePublication YearGoogle Scholar Citation Count
DATF: a database of Arabidopsis transcription factors2005164
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tagsamino acid sequence arabidopsis proteins database management systems molecular sequence data plant proteins protein databases transcription factors

DDBJDatabase Content

http://www.ddbj.nig.ac.jp [open in a new window]

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DNA > Databases

The DNA Data Bank of Japan (DDBJ) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. A new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Other improvements include improved content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based analytical system from sequencing reads, the DDBJ Read Annotation Pipeline.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments20123
DDBJ progress report201115
DDBJ launches a new archive database with analytical tools for next-generation sequence data201031
NAR Database Issue 2010NAR Database Issue 2011
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external linksLink on Twitter Link on Wikipedia
tagsalgorithms amino acid sequence animals bacterial genome computational biology genetic databases genomics humans japan molecular sequence annotation nucleic acid databases patents as topic protein databases

DIALIGNTool Content

http://bibiserv.techfak.uni-bielefeld.de/dialign/ [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments

Multiple alignment program which assembles a global sequence alignment from gap-free local pairwise alignments. This method could be especially useful when comparing large sequences that have only local similarities.

links directory index: 1034
TitlePublication YearGoogle Scholar Citation Count
DIALIGN: multiple DNA and protein sequence alignment at BiBiServ2004176
Fast and sensitive multiple alignment of large genomic sequences2003153
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment1999705
NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence amino acid sequence homology animals chickens computational biology dna sequence analysis genome humans leukemia mice molecular sequence data neoplasm dna neoplasm genes nucleic acid regulatory sequences protein sequence analysis proteins rats sensitivity and specificity sequence alignment software validation stem cells tetraodontiformes zebrafish

DISULFINDTool Content

http://disulfind.dsi.unifi.it/ [open in a new window]

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Protein > Biochemical Features
Protein > Sequence Features

DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.

This content is being maintained by paolo.frasconi.

links directory index: 252
TitlePublication YearGoogle Scholar Citation Count
MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence20111
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence200825
DISULFIND: a disulfide bonding state and cysteine connectivity prediction server200689
Disulfide connectivity prediction using recursive neural networks and evolutionary information2004137
NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence artificial intelligence binding sites computational biology computer simulation cysteine disulfide bridges disulfides gene expression profiling histidine machine learning metalloproteins molecular evolution molecular sequence data neural networks (computer) protein binding protein databases protein sequence analysis proteins sequence alignment

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