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This list of protein subcellular localisation prediction tools includes software, databases, and web services that are used for protein subcellular localization prediction. Some tools are included that are commonly used to infer location through predicted structural properties, such as signal peptide or transmembrane helices , and these tools ...
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
Simple Modular Architecture Research Tool (SMART) is a biological database that is used in the identification and analysis of protein domains within protein sequences. [ 1 ] [ 2 ] SMART uses profile-hidden Markov models built from multiple sequence alignments to detect protein domains in protein sequences.
The development of protein domain databases such as Pfam (Protein Families Database) [10] allow us to find known domains within a query sequence, providing evidence for likely functions. The dcGO website [ 11 ] contains annotations to both the individual domains and supra-domains (i.e., combinations of two or more successive domains), thus via ...
The HH-suite comes with a number of pre-built profile HMMs that can be searched using HHblits and HHsearch, among them a clustered version of the UniProt database, of the Protein Data Bank of proteins with known structures, of Pfam protein family alignments, of SCOP structural protein domains, and many more.
PredictProtein (PP) is an automatic service that searches up-to-date public sequence databases, creates alignments, and predicts aspects of protein structure and function. Users send a protein sequence and receive a single file with results from database comparisons and prediction methods.
Functional annotation is provided to proteins from multiple resources. Functional prediction and analysis of domain architectures is available from the Gene3D website. CDD Conserved Domain Database is a protein annotation resource that consists of a collection of annotated multiple sequence alignment models for ancient domains and full-length ...
Name Method description Type Link Initial release RaptorX-SS8 : predict both 3-state and 8-state secondary structure using conditional neural fields from PSI-BLAST profiles ...