> > Sequence Features

Sequence Features

This section includes links to tools which can predict primary sequence features for the residues of a protein.

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Found 48 links

Displaying 15 links

AnalyCysDatabase Content

http://bioinformatics.univ-reunion.fr/analycys/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Sequence Features

AnalyCys is database for the analysis of conservation and conformation of disulphide bonds in SCOP structural families. This database has a wide range of applications including mapping of disulphide bond mutation patterns, identification of cysteine residues and disulphide bonds important for folding and stabilization, modeling of protein structures and in protein engineering.

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BindNTool Content

http://bioinformatics.ksu.edu/bindn/

Protein > Domains and Motifs
Protein > Sequence Features

BindN takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs).

NAR Web Server Issue 2006
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tagsamino acids artificial intelligence binding sites dna dna-binding proteins molecular models protein sequence analysis rna-binding proteins

BioBayesNetTool Content

http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Sequence Features

BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence automated pattern recognition bayes theorem binding sites chemical models computational biology computer simulation dna sequence analysis genetic models molecular models molecular sequence data protein binding protein conformation protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship transcription factors

Bioinformatics ToolkitTool Content

http://toolkit.tuebingen.mpg.de/

DNA > Annotations
DNA > DNA and Genomic Analysis
DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Localization and Targeting
Protein > Molecular Dynamics and Docking
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

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CanPredictTool Content

http://www.cgl.ucsf.edu/Research/genentech/canpredict/

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Sequence Features

CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.

NAR Web Server Issue 2007
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tagsalgorithms alleles amino acids computational biology expressed sequence tags genetic predisposition to disease humans missense mutation neoplasm dna neoplasms single nucleotide polymorphism tumor cell line

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

NAR Web Server Issue 2005
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tagsprotein sequence analysis systems integration

CCRXPTool Content

http://ccrxp.netasa.org

Protein > 3-D Structural Features
Protein > Sequence Features

A tool for the detection of conserved residue clusters from an input PDB file. Structural properties of each residue, such as solvent accessibility (ASA), secondary structure, conservation score etc. and the conserved residue clusters are also computed.

This content is being maintained by shandar.

NAR Web Server Issue 2010
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tagsclustered residues consensus sequence conservation score dna-binding proteins hot spots interface multiprotein complexes mutation proteins rna-binding proteins solvent accessibility

CLIPTool Content

http://clip.med.yale.edu/selection

Protein > Sequence Features

CLIP web server detects selection in immunoglobulin sequences. Web server features include V(D)J germline segment identification with IMGT-alignment, batch submission of sequences and integration of test statistics.

NAR Web Server Issue 2011
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ConSeqTool Content

http://conseq.bioinfo.tau.ac.il/

Protein > 3-D Structural Features
Protein > Phylogeny Reconstruction
Protein > Sequence Features

ConSeq is a tool for predicting functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of structural importance are often conserved and located in the protein core. A multiple sequence alignment is used to predict the relative solvent accessibility state and the evolutionary rate at each residue. ConSeq has been integrated into ConSurf (2010).

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tagsalgorithms amino acid sequence amino acid sequence homology amino acid substitution amino acids molecular sequence data protein sequence analysis proteins sequence alignment structure-activity relationship

CRPDatabase Content

http://fasta.bioch.virginia.edu/crp/

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.

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

DiANNATool Content

http://bioinformatics.bc.edu/clotelab/DiANNA/

Protein > Biochemical Features
Protein > Sequence Features

DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.

NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsalgorithms artificial intelligence binding sites chemical models computer simulation cysteine disulfides neural networks (computer) oxidation-reduction protein binding protein conformation protein interaction mapping protein sequence analysis proteins secondary protein structure sequence alignment structure-activity relationship

DISULFINDTool Content

http://disulfind.dsi.unifi.it/

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.

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

DrugScorePPITool Content

http://cpclab.uni-duesseldorf.de/dsppi

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Features

DrugScorePPI web server performs alanine scanning within a given protein-protein complex in silico. Useful for guiding biological experiments and in the development of protein-protein interaction modulators.

NAR Web Server Issue 2010
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tagsalanine multiprotein complexes mutation protein interaction mapping ral gtp-binding proteins ral guanine nucleotide exchange factor

E1DSTool Content

http://e1ds.ee.ncku.edu.tw/

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Features

E1DS is a web server for enzyme catalytic site prediction. Annotation of enzymes is made using a novel pattern mining algorithm that discovers long sequence motifs.

NAR Web Server Issue 2008
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tagsamino acid sequence catalytic domain conserved sequence enzymes protein sequence analysis

eBioinformaticsResource Content

http://www.ebioinformatics.org/

DNA > DNA and Genomic Analysis
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Presentation and Format
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.

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Tags associated with subcategory 'Protein/Sequence Features'

protein sequence analysis proteins sequence alignment algorithms amino acid sequence computational biology binding sites animals molecular models molecular sequence data amino acid sequence homology dna sequence analysis protein conformation humans amino acids reproducibility of results protein databases artificial intelligence nucleic acid regulatory sequences dna documentation database management systems computer systems transcriptional regulatory elements genetic predisposition to disease chlamydophila pneumoniae cluster analysis factual databases multigene family theoretical models genomics multimedia open reading frames nucleotides nucleic acid databases fuzzy logic genetic databases genome monoclonal antibodies tertiary protein structure phosphotyrosine antibody specificity cattle phosphothreonine post-translational protein processing protein precursors regression analysis lysine methylation conserved sequence epitope mapping software design stochastic processes streptomyces sequence analysis peptides epitopes mice phylogeny pancreatic ribonuclease variola virus poxviridae secondary protein structure radioactive tracers recombinant proteins amino acid substitution protein interaction mapping scorpion venoms bacterial proteins cysteine disulfides statistical data interpretation molecular evolution neural networks (computer) protein binding protein folding statistical models structure-activity relationship genetic models computer simulation sensitivity and specificity automated pattern recognition bayes theorem chemical models bacterial genome tumor cell line viral dna viral genes viral genome viral proteins neuropeptides vaccinia virus programming languages reference standards technology transfer thermoplasma hydrogen bonding mutation missense mutation neoplasm dna neoplasms