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Links tagged with 'peptides'

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3didDatabase Content

http://3did.irbbarcelona.org/

Protein > Databases

The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The 3did web server visualizes these interfaces along with atomic details of individual interactions using Jmol.

NAR Database Issue 2011
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tagsmolecular models peptides protein databases protein interaction domains and motifs protein interaction mapping

CAMPDatabase Content

http://bicnirrh.res.in/antimicrobial

Other Molecules > Databases

Collection of Anti-Microbial Peptides (CAMP) is a free online database that is manually curated and currently holds 3782 antimicrobial sequences. These sequences are divided into experimentally validated (patents and non-patents: 2766) and predicted (1016) datasets based on their reference literature. Information like source organism, activity (MIC values), reference literature, target and non-target organisms of AMPs are captured in the database. Prediction and sequence analysis tools, including BLAST, are integrated in the database.

NAR Database Issue 2010
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tagsalgorithms anti-infective agents antimicrobial cationic peptides bacterial genome computational biology genetic databases humans nucleic acid databases peptides protein databases reproducibility of results

DeNovoIDDatabase Content

http://proteomics.mcw.edu/denovoid/

Protein > Proteomics

DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments.

NAR Web Server Issue 2005
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tagsalgorithms amino acids mass spectrometry peptides protein databases protein sequence analysis proteomics

DILIMOTTool Content

http://dilimot.embl.de/

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

Discovery of Linear Motifs (DILIMOT) is a server for finding short (3-8 amino acids) over-represented peptide patterns in a set of proteins.

NAR Web Server Issue 2006
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tagsamino acid motifs amino acid sequence animals binding sites genome humans microtubule-associated proteins molecular models molecular sequence data peptides protein binding protein kinases protein sequence analysis protein sorting signals proteins tertiary protein structure

EpiToolKitTool Content

http://www.epitoolkit.org

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Molecular Dynamics and Docking

A suite of tools for immunological research. EpiToolKit offers a variety of prediction methods that may be run simultaneously for predicting MHC Class I and II ligands, and minor histocompatibility antigens. The influence of sequence polymorphisms or mutations on potential T-cell epitopes may also be examined.

NAR Web Server Issue 2008
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tagsacetaminophen child computational biology dosage forms drug packaging france genetic polymorphism histocompatibility antigens humans ligands mutation neoplasm antigens non-narcotic analgesics oral administration peptides poison control centers poisoning protein sequence analysis t-lymphocyte epitopes

eShadowTool Content

http://eshadow.dcode.org/

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

A tool for phylogenetic shadowing of multiple sequences from closely related species. This analyses of multiple sequence alignments can be used to predict putative functional elements.

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tagsanimals computational biology conserved sequence exons genetic databases humans intergenic dna papio peptides proteins software design tertiary protein structure

FASTA ProgramsTool Content

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

Sequence Comparison > Similarity Searching

Sequence retrieval and comparison tools.

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tagsadrenergic receptors algorithms amino acid sequence animals antigen receptors base sequence dna eye proteins gene library globins humans information systems molecular sequence data nucleic acid sequence homology peptides proteins rod opsins transforming growth factors

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

IEDB-ARTool Content

http://tools.immuneepitope.org

Human Genome > Health and Disease
Protein > Do-it-all Tools for Protein

The Immune Epitope Database Analysis Resource (IEDB-AR) is a collection of tools for the prediction and analysis of immune epitopes. Tools include B-cell and T-cell epitope prediction and epitope analysis tools.

NAR Web Server Issue 2008
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tagsb-lymphocyte epitopes factual databases histocompatibility antigens class i histocompatibility antigens class ii peptides proteins t-lymphocyte epitopes

Immune Epitope DatabaseDatabase Content

http://tools.immuneepitope.org/

Human Genome > Databases
Protein > Databases

The Immune Epitope Database (IEDB) provides a catalog of experimentally characterized B and T cell epitopes, as well as data on Major Histocompatibility Complex (MHC) binding and MHC ligand elution experiments. The database represents the molecular structures recognized by adaptive immune receptors and the experimental contexts in which these molecules were determined to be immune epitopes. Epitopes recognized in humans, nonhuman primates, rodents, pigs, cats and all other tested species are included. Both positive and negative experimental results are captured. The database can be queried by epitope structure, source organism, MHC restriction, assay type or host organism, among other criteria.

NAR Database Issue 2010
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tagsanimals communicable diseases computational biology epitopes genetic databases humans immune system immunogenetics major histocompatibility complex peptides protein databases proteins

MaXIC-QTool Content

http://ms.iis.sinica.edu.tw/MaXIC-Q

Protein > Proteomics

The MaXIC-Q web server performs various quantification analyses on large-scale datasets generated from proteomics studies using isotope labeling. For input MS data, output is given in projected ion mass spectrum and extracted ion chromatograph which can be used to generate other calculations (e.g. ion abundances and peptide-protein ratios.

NAR Web Server Issue 2009
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tagscomputational biology endothelial cells isotope labeling liquid chromatography mass spectrometry nitric acid peptides proteins reproducibility of results statistical data interpretation

MetaMHCTool Content

http://www.biokdd.fudan.edu.cn/Service/MetaMHC.html

Human Genome > Annotations
Protein > Domains and Motifs
Protein > Localization and Targeting

MetaMHC integrates the outputs of leading MHC binding predictors. MHC class I and II peptides binding are predicted.

This content is being maintained by Xihao Hu.

NAR Web Server Issue 2010
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tagsanimals binding sites histocompatibility antigens class i histocompatibility antigens class ii humans mice peptides

ModBaseDatabase Content

http://salilab.org/modbase

Protein > Databases

ModBase is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment. ModBase allows users to update comparative models on demand, and request modeling of additional sequences through an interface to the ModWeb modeling server. Recently developed associated resources include the SALIGN server for multiple sequence and structure alignment, the ModEval server for predicting the accuracy of protein structure models, the PCSS server for predicting which peptides bind to a given protein and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles.

NAR Database Issue 2011
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tagsbacterial proteins molecular models peptides protein databases protein interaction mapping protein structural homology proteins sequence alignment small angle scattering tertiary protein structure x-ray diffraction

MODiTool Content

http://prix.uos.ac.kr/research.jsp

Protein > Biochemical Features
Protein > Proteomics

Modi is a tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide.

NAR Web Server Issue 2006
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tagsmass spectrometry peptides post-translational protein processing protein databases protein sequence analysis

MODPROPEPTool Content

http://www.nii.res.in/~narendra/PROT_PEP_INTERACTION/index.html

Protein > 3-D Structure Prediction
Protein > Domains and Motifs

MODPROPEP is a server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.

NAR Web Server Issue 2007
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tagsalgorithms animals computational biology computer simulation humans major histocompatibility complex peptides protein conformation protein databases proteins x-ray crystallography