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Links tagged with 'post-translational protein processing'

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AntigenDBDatabase Content

http://www.imtech.res.in/raghava/antigendb/

Human Genome > Databases

AntigenDB contains 500 antigens to pathogenic species curated from the literature and other immunological resources. In AntigenDB, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post translational modifications, where available. AntigenDB also provides links to major internal and external databases.

This content is being maintained by raghavagps.

NAR Database Issue 2010
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tagsantigens communicable diseases computational biology epitopes genetic databases humans immune system immunogenetics lymphocytes peptide mapping post-translational protein processing protein databases tertiary protein structure

CPLA 1.0Database Content

http://cpla.biocuckoo.org

Protein > Databases

Compendium of protein lysine acetylation (CPLA) database is a resource of manually curated lysine acetylated substrates with their sites.

This content is being maintained by little_xian.

NAR Database Issue 2011
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tagsacetylation histone acetyltransferases histone deacetylases humans lysine post-translational protein processing protein databases proteins systems integration

Human Protein Reference DatabaseDatabase Content

http://www.hprd.org/

Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

The Human Protein Reference Database (HPRD) is a centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in HPRD is curated by experts, who manually extract it from published literature.

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tagsbrca1 protein computational biology controlled vocabulary disease genomics humans macromolecular substances medical genetics post-translational protein processing protein binding protein databases protein interaction mapping proteins proteome proteomics quaternary protein structure substrate specificity tertiary protein structure

InterProDatabase Content

http://www.ebi.ac.uk/interpro/index.html

Protein > Domains and Motifs

Integrated database of commonly used signature databases (e.g. PROSITE, PRINTS, SMART, Pfam, ProDom); text- and sequence-based searches.

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tagsalgorithms amino acid repetitive sequences animals computational biology factual databases humans information services metabolic networks and pathways post-translational protein processing protein databases protein sequence analysis proteins search engine sequence alignment systems integration tertiary protein structure

MeMoTool Content

http://www.bioinfo.tsinghua.edu.cn/%7Etigerchen/memo.html

Protein > Sequence Features

Methylation Modification Prediction Server (MeMo) is a server that predicts arginine and lysine sites that undergo methylation using a support vector machine (SVM).

NAR Web Server Issue 2006
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tagsarginine artificial intelligence lysine methylation post-translational protein processing proteins

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

PDBSiteScanTool Content

http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html

Protein > 3-D Structural Features

PDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.

NAR Web Server Issue 2004
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tagsbinding sites catalytic domain hydrolases intracellular signaling peptides and proteins molecular models oncogene proteins post-translational protein processing proteins tertiary protein structure

PeptideMassTool Content

http://us.expasy.org/tools/peptide-mass.html

Protein > Biochemical Features

Cleaves a protein sequence with a chosen enzyme and computes masses of the generated peptides.

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tagsamino acid sequence factual databases humans molecular sequence data peptides post-translational protein processing

PHOSIDA 2011Database Content

http://www.phosida.com

Protein > Databases

PHOSIDA database manages posttranslational modification sites of various species ranging from bacteria to human. It contains phosphorylated, N-glycosylated or acetylated sites. All sites are obtained from high-resolution mass spectrometric data. PHOSIDA is comprised of three main components: the database environment, the prediction platform and the toolkit section. The database environment integrates and combines high-resolution proteomic data with multiple annotations. High-accuracy species-specific phosphorylation and acetylation site predictors, trained on the modification sites contained in PHOSIDA, allow the in silico determination of modified sites on any protein on the basis of the primary sequence. The toolkit section contains methods that search for sequence motif matches or identify de novo consensus, sequences from large scale data sets.

NAR Database Issue 2011
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tagshumans post-translational protein processing protein databases protein sequence analysis proteomics species specificity

Phospho.ELMDatabase Content

http://phospho.elm.eu.org/

Protein > Domains and Motifs

Database of experimentally verified phosphorylation sites in eukaryotic proteins. Annotations are done manually and database entries come from and are linked back to scientific literature. Phospho.ELM incorporates the data formerly found in PhosphoBase.

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tagsanimals binding sites humans mice phosphorylation post-translational protein processing protein databases proteins rats research design

ProKwareTool Content

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

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

ProKware is a tool for investigating protein structural properties such as domains, functional sites, and post-translational modifications. To use some features a stand-alone piece of software is necessary; currently available for windows only.

NAR Web Server Issue 2006
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tagsbinding sites molecular models post-translational protein processing protein databases proteins systems integration tertiary protein structure

ProMoSTTool Content

http://proteomics.mcw.edu/promost

Expression > Protein Expression
Protein > Biochemical Features
Protein > Protein Expression
Protein > Proteomics

ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images.

This content is being maintained by halligan.

NAR Web Server Issue 2004
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tagsalgorithms gel electrophoresis isoelectric point molecular weight post-translational protein processing proteins

ProSight PTMTool Content

http://prosightptm2.scs.uiuc.edu/

Protein > Biochemical Features
Protein > Proteomics

ProSight PTM allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using data from the \'Top-Down\' tandem mass spectrometry (MS/MS) approach.

NAR Web Server Issue 2004NAR Web Server Issue 2007
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tagsalternative splicing amino acid sequence animals automatic data processing computational biology genetic polymorphism humans mass spectrometry molecular sequence data post-translational protein processing programming languages protein databases protein sequence analysis proteins ribosomal proteins saccharomyces cerevisiae proteins sequence tagged sites

SUMOspTool Content

http://sumosp.biocuckoo.org/

Protein > Domains and Motifs

SUMOylation Sites Prediction (SUMOsp) predicts sites for sumoylation, a reversible post-translational modification of proteins by the small ubiquitin-related modifiers (SUMO).

NAR Web Server Issue 2006
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tagsalgorithms computational biology post-translational protein processing proteins small ubiquitin-related modifier proteins

The Mendel SiteTool Content

http://mendel.imp.ac.at/

Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting

The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.

NAR Web Server Issue 2003
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tagsacyltransferases amino acid motifs animals eukaryotic cells fungal proteins glycine glycosylphosphatidylinositols lipid metabolism molecular sequence data myristic acids peroxisomes plant proteins post-translational protein processing protein sequence analysis protein sorting signals proteins protozoan proteins viral proteins