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EFICAz / Enzyme Function Inference by a Combined Approach
Allows users to study the proteomic scale inference of enzyme function. EFICAz can identify functionally discriminating residue (FDR) as residues that discriminate the members of a homo-functional family from a hetero-functional family. It combines the prediction from four independent methods, namely: (1) CHIEFc family-based (FDR) identification, (2) multiple PFAM-based FDR recognition, (3) CHIEFc SIT evaluation and (4) high-specificity multiple PROSITE patterns.
Predicts functional annotations. AnnoLite annotates the structures processed by DBAli. The web application searches the DBAli database for structurally similar proteins and collects their known annotations. It annotates the input protein structure with CATH and SCOP fold assignments, EC numbers, InterPro entries, PFAM families and Gene Ontology (GO) and codes. The software can annotate a structure for all of the functional properties, with the exception of the GO cellular component term.
Allows global comparison and research for small dissimilar fragments. MCQ4Structures applies mean of circular quantities (MCQ) for the purpose of structure similarity identification. It is based on trigonometric representation of the molecule 3D structure and the inter-molecular distance measured as MCQ. This tool allows to aggregate over any number of differences computed for pairs of corresponding angles. The software also implements the LCS-TA algorithm, that finds fragments displaying high similarity in torsion angle space.
The LabelHash Server
A server and tools designed for largescale substructure comparison. The LabelHash Server predicts the function of unknown proteins. The algorithm consists of two stages: (i) a preprocessing stage (the algorithm builds up lookup tables for n-tuples of residues that occur in a set of target structures) and (ii) a matching stage (the algorithm first looks for partial matches of size n and incrementally expands these partial matches to complete matches in a depth-first fashion).
A web server for detailed estimation of similarities between all pairs of 3D patterns detected in any two given protein structures. Geomfinder is composed of four main steps: (i) generates on each protein a virtual grid of coordinates which represents the initial location to find the 3D patterns; (ii) all possible 3D patterns occurring in each of the proteins of interest are detected, using as reference the virtual grid already generated; (iii) generates a list of four descriptors for each 3D pattern identified; (iv) makes use of the descriptors previously estimated to calculate a single similarity score among any possible pair of 3D patterns found in each queried protein.
PBE / Protein Block Expert
Allows users to perform comparison and analysis for protein structure. PBE offers a platform composed of 10 tools which can accomplish various tasks such as (i) Encode protein structure into PBs sequence; (ii) Compare structure between a pair of proteins using PB description using both local and global alignment algorithms (iii) Mine a databank derived from SCOP, to detect proteins with similar fold (iv) Browse a database of preprocessed PB sequences and pairwise alignments at family and superfamily levels.
Provides efficient analysis of similar protein tertiary substructures. ProteMiner-SSM is a web server that carries out analysis in two steps. In the first step, a filtering process based on an efficient kernel density estimation algorithm is invoked to identify the crucial tertiary substructures on the contour of the protein that the analysis should focus on. In the second step, the geometric hashing algorithm in computer graphics (12,13) is invoked to compare the crucial substructures of the target protein and the binding/ active site of the reference protein.
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