Proteins
From MyBio
letobopa
| DPL Forum: Too few categories! |
[edit] Related subcategories
- Signal scan
- Physicochemical properties of proteins and peptides
- Domains
- Protein structure
- Proteomics
- Protein databases
- Protein sequence databases
- Protein sequence alignment
- Functional Sites
- Protein classification
- Protein Disorder
- Composition
- Peptides
- Protein Engineering
- Enzymes
- Mutant Analysis
- Features
- Proteins by function
- Meta tools
- Post-translational modifications
- NMR
- Motif or Pattern Search
[edit] Proteins - Quick Links
| Structural Classification of Proteins (SCOP) | [1] | |
| The Universal Protein Resource (UniProt) | [2] | |
| WinPep | MetaPP | |
| miniPedant | HarvESTer | |
| CLC bio: Protein Workbench |
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[edit] Proteins - Web Resources
| Structural Classification of Proteins (SCOP) | Created by manual inspection and automated methods aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins. | <thumbnail>http://scop.berkeley.edu/</thumbnail> |
| The Universal Protein Resource (UniProt) | UniProt aims to provide the scientific community with a free, stable, single, centralized, authoritative resource for protein sequences and functional information, backed by a consortium of Swiss-Prot, TrEMBL and PIR protein databases. UnProt is built by manual curation of protein sequences assisted by computational analysis and sequence archiving. UniProt aims to be a fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database has two sections, corresponding to the familiar Swiss-Prot (fully manually curated entries) and TrEMBL (enriched with automated classification). For convenient sequence search, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases.  New feature (2006): metagenomic and environmental sequences
| <thumbnail>http://www.ebi.uniprot.org/index.shtml</thumbnail> |
WinPep
A versatile tool for the analysis of aminoacid sequences. Determination of length and amino acid composition. Calculation of the molecular weight. Estimation of the isoelectric point (IEP). Estimation of molar absorption coefficients. Batch analysis of multiple sequences. Simulation of sequence specific cleavage. Identification of potential posttranslational modifications. Searching for sequence motifs. Display of amino acid sequences as helical wheels. Display of hydropathy plots of sequences. Display of the domain structure of proteins.
MetaPP
Web interface to many public protein structure and function prediction servers. META-PP provides access to a selected set of high-quality servers in the areas of comparative modelling, threading/fold recognition, secondary structure prediction and more specialized fields like function prediction, homology modelling, secondary structure, threading and transmembrane helices.
miniPedant
miniPEDANT displays primary information such as statistical evaluation of protein properties, best BLAST hits, multiple alignment to homologous sequences, presence of sequences domain, domain patterns etc. Additionally, secondary structures and trans-membrane segments are predicted and a 3D-structure is assigned to the sequence wherever possible. The core components of miniPEDANT stem from PEDANT, but the added flexibility of the miniPEDANT system allows the rapid development of specific databases, containing highly specific sequence derived data for core research within the biological sciences.
HarvESTer
HarvESTerTM is a sophisticated, high throughput clustering and assembly tool with a series of flexible modules that address specific issues of EST (Expressed Sequence Tag) data processing. ESTs, as well as full-length transcript data (cDNAs), can be combined to obtain consensus sequences representing the expressed gene set of a specific organism. Due to the massive amount and diversity of data, each project requires a customized scheme as well as increasing computational power. HarvESTer meets these needs by coupling optimized algorithms with intelligent parallelization and highly flexible process configurations. HarvESTer is platform independent utilizing JavaTM and HTML user interfaces.
CLC bio: Protein Workbench
Creates a software environment enabling advanced protein sequence analyses, 3D molecule view, transmembrane helix prediction, secondary structure predictions, identification of protein domains through PFAM domain searches and prediction of signal peptides
