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Links tagged with 'probability'

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COILSTool Content

http://www.ch.embnet.org/software/COILS_form.html

Protein > 2-D Structure Prediction

Prediction of coiled coil regions.

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tagsamino acid sequence amino acids animals factual databases humans probability protein conformation proteins

eProbalignTool Content

http://probalign.njit.edu/probalign/login

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology animals computational biology computer simulation dna genetic databases humans molecular sequence data probability protein sequence analysis sequence alignment software design statistical models temperature thermodynamics

GENSCANTool Content

http://genes.mit.edu/GENSCAN.html

DNA > Gene Prediction

Identification of complete gene structures in genomic DNA.

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tagsanimals dna dna sequence analysis exons genes genetic models genetic promoter regions genetic techniques genetic transcription human genome humans introns markov chains molecular sequence data nucleic acid repetitive sequences probability protein biosynthesis proteins rna splicing vertebrates

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

NAR Web Server Issue 2003NAR Web Server Issue 2004
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

ICGEBnet Protein ToolsTool Content

http://www.icgeb.org/protein/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

ICGEBnet Protein Tools is a resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) and/or depth (DPX) indexes in 3D models.

NAR Web Server Issue 2005
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tagsalgorithms animals chemical models cluster analysis computational biology crystallography humans interferon alfa-2a molecular evolution molecular models molecular structure probability programming languages protein conformation protein databases protein folding protein interaction mapping proteins secondary protein structure sensitivity and specificity sequence homology serpins tertiary protein structure trypsin

iSPOTTool Content

http://cbm.bio.uniroma2.it/ispot/

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence animals binding sites computational biology factual databases humans ligands molecular models molecular sequence data multigene family peptide fragments peptide library probability protein binding protein databases protein sequence analysis proteins sequence alignment src homology domains substrate specificity tertiary protein structure

KinasePhos 2.0Tool Content

http://kinasephos2.mbc.nctu.edu.tw/

Protein > Domains and Motifs

KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.

NAR Web Server Issue 2007
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tagscatalytic domain computational biology computer simulation markov chains neural networks (computer) phosphoproteins phosphorylation probability protein kinases protein sequence analysis sensitivity and specificity

MASCOT (Matrix Science)Tool Content

http://www.matrixscience.com/

Protein > Biochemical Features
Protein > Proteomics

Protein identification by peptide mass; excellent documentation; incorporates code from MOWSE but allows more search methods on more sequence databases.

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tagsamino acid sequence amino acids factual databases mass spectrometry molecular sequence data molecular weight nucleic acids probability protein biosynthesis proteins

ModellerTool Content

http://salilab.org/modeller/

Protein > 3-D Structure Prediction

Homology or comparative modeling of 3D protein structures.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology animals bacterial proteins biological models carrier proteins computer simulation enzymes factual databases genetic models genome genomics humans kallikreins l-lactate dehydrogenase mathematics molecular models molecular sequence data pancreatic elastase probability protein conformation protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure theoretical models thermodynamics tissue kallikreins trichomonas vaginalis trypsin

PfoldTool Content

http://www.daimi.au.dk/~compbio/pfold

RNA > Structure Prediction, Visualization, and Design

The Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.

NAR Web Server Issue 2003
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tagsalgorithms bacterial rna base sequence biological evolution catalytic rna computational biology computer simulation endoribonucleases molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid sequence homology probability reproducibility of results ribonuclease p rna rna sequence analysis sequence alignment stochastic processes time factors

PhobiusTool Content

http://phobius.sbc.su.se/

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

Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.

This content is being maintained by lukall.

NAR Web Server Issue 2007
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tagsalgorithms artificial intelligence computational biology computer simulation cytoplasm markov chains membrane proteins molecular models probability programming languages protein conformation protein databases protein sorting signals proteomics secondary protein structure statistical models theoretical models

PSATool Content

http://bmerc-www.bu.edu/psa/request.htm

Protein > 2-D Structure Prediction

Prediction of probable secondary structures and fold-class; good for visualizing amphipathic helices, where present.

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tagsamino acid sequence chemical models flavodoxin markov chains mathematics molecular sequence data molecular structure probability proteins secondary protein structure structural models tertiary protein structure thioredoxins

Servers at University College LondonTool Content

http://bioinf.cs.ucl.ac.uk/web_servers/

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

SfoldTool Content

http://sfold.wadsworth.org

DNA > Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design

Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.

NAR Web Server Issue 2004
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tagsalgorithms animals antisense oligonucleotides antisense rna base sequence bayes theorem binding sites catalytic rna computational biology drug design escherichia coli molecular sequence data nucleic acid conformation phylogeny probability protozoan rna rabbits ribosomal rna rna rna stability small interfering rna spliced leader rna statistical distributions statistical models tetrahymena thermophila thermodynamics transfer rna xenopus laevis

SH3-HunterTool Content

http://cbm.bio.uniroma2.it/SH3-Hunter/

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.

This content is being maintained by enricoferraro.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence animals artificial intelligence automated pattern recognition binding sites chemical models computational biology computer simulation factual databases humans ligands molecular models molecular sequence data multigene family neural networks (computer) peptide fragments peptide library peptides probability protein binding protein interaction mapping protein sequence analysis proteins proteome sensitivity and specificity sequence alignment src homology domains structure-activity relationship substrate specificity tertiary protein structure