The TMPred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occurring transmembrane proteins. The prediction is made using a combination of several weight matrices for scoring.
We predicted the similarity of query proteins to proteins in the human proteome.
ProtParam is a tool that allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user-entered protein sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index, and grand average of hydropathicity (GRAVY).
AllerBase is a comprehensive knowledge base of allergens and allergen-related features such as IgE-binding epitopes, IgE antibodies, and cross-reactivity. The experimentally validated data on allergens and their features have been compiled by extensive search and manual curation from the published literature along with immunological, allergen, and primary bioinformatics databases. The database provides in-depth coverage of allergens and related data with cross-references to primary, immunological, and allergen databases. We predicted the similarity of query protein to the AllerBase database.
FungalRV provides an adhesin predictor software tool to predict human pathogenic fungal adhesins and adhesin-like proteins.
Essential genes are those indispensable for the survival of an organism and therefore are considered a foundation of life. DEG hosts records of currently available essential genomic elements, such as protein-coding genes and non-coding RNAs, among bacteria, archaea, and eukaryotes. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field, synthetic biology.
The virulence factor database (VFDB) is an integrated and comprehensive online resource for curating information about virulence factors of bacterial pathogens. Since its inception in 2004, VFDB has been dedicated to providing up-to-date knowledge of VFs from various medically significant bacterial pathogens. We predicted the similarity of query protein to virulence factors.
The SignalP 5.0 server predicts the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria, and Eukarya.
Gut microbiota, gut flora, or microbiome are the microorganisms including bacteria, archaea, and fungi that live in the digestive tracts of humans and other animals including insects. We predicted the similarity of query protein to GutfloraDB.
TargetP-2.0 server predicts the presence of N-terminal pre-sequences: signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP), or thylakoid luminal transit peptide (luTP). For the sequences predicted to contain an N-terminal pre-sequence, a potential cleavage site is also predicted.
NetMHC 3.4 server predicts binding of peptides to a number of different HLA alleles using artificial neural networks (ANNs).
NetChop is a tool to predict cleavage sites of the human proteasome. The NetChop algorithm uses a neural network trained on human proteasome data.
NetCTL 1.0 server predicts CTL epitopes in protein sequences. The method integrates prediction of peptide MHC binding, proteasomal C terminal cleavage, and TAP transport efficiency. The server allows for predictions of CTL epitopes restricted to 10 MHC supertype. MHC binding and proteasomal cleavage are performed using artificial neural networks. TAP transport efficiency is predicted using a weight matrix.
PSORTb is a program for bacterial protein subcellular localization prediction. The latest version of PSORTb v3.0 handles archaeal sequences as well as Gram-positive and Gram-negative bacterial sequences.
The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity, and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes.