1 - 24 of 24 results

HOMCOS / HOMology modeling of COmplex Structure

Searches and models the 3D complexes for all molecules in the Protein Data Bank (PDB) (proteins, nucleic acids, small compounds and metal ions). HOMCOS stores their binding relationships in a dedicated database. Five services are available for users: Modeling a Homo Protein Multimer, Modeling a Hetero Protein Multimer, Protein-Compound Complex, Searching Contact Molecules for a Query Protein and Searching Contact Molecules for a Query Compound. HOMCOS employs the standard program BLAST for finding protein templates and the program KCOMBU for finding compound templates.


Aims to fill the gap between the fast and widely used homology search programs, such as BLAST, PSI-BLAST, or HMMer/Pfam, and the very sensitive and accurate but rather inflexible and slow automated protein structure prediction servers. HHpred is therefore mainly meant to be used as an interactive function and structure prediction server, allowing, for example, to search various databases, to select templates manually, or to correct errors in the proposed target-template alignment. HHPred is part of the HH-suite and is available online or can be downloaded for local use.

LRFragLib / Logistic Regression based Fragment Library

A fragment-library-construction algorithm. LRFragLib improves the detection of near-native low-homology fragments of 7-10 residues, using a multi-stage, flexible selection protocol. Based on logistic regression scoring models, LRFragLib outperforms existing techniques by achieving a significantly higher precision and a comparable coverage on recent CASP protein sets in sampling near-native structures. The method also has a comparable computational efficiency to the fastest existing technique with substantially reduced memory usage.

Al-Eigen / contact Map Overlap by Alignement of Eigenvectors

Addresses the contact map overlap (CMO) problem. Al-Eigen is a heuristic algorithm that computes an overlap of two contact maps by performing a global alignment based on few eigenvectors. The computing time does not depend on the number of contacts in the map and then on the contact threshold, but uniquely on the protein length and on the number of eigenvectors considered. It performs the task of structural similarity detection, also with highly perturbed contact maps, at least at the SCOP family level.

ORION / Optimized protein fold RecognitION

A web app for homology detection and template-based modeling. ORION relies on a better description of the local protein structure to boost distantly protein detection. ORION algorithm is divided into three main steps: (i) preparation of the multiple sequence alignment (MSA) of query -potential- homologs, (ii) generation of query profile and (iii) alignment of the query profile to templates profiles from a databank. Comparisons with similar servers show that ORION web server is also a powerful tool for the protein structure prediction.

ACDC / Attribute Clustering Dependent Communities

Detects community structure in protein sequence similarity network (SSN). ACDC is an unsupervised method that utilizes attribute vector clustering and excludes user-tunable parameters. The software serves as a community detection method for multiplex networks. It was applied successfully to gold standard datasets for which “ground truth” community structure is known. ACDC can be used for community detection in large sequence datasets, particularly once parallel implementations have been incorporated.

CMASA / Contact MAtrix based local Structural Alignment algorithm

Detects local protein structural similarity. CMASA is an accurate and sensitive method which can not only search the similar functional proteins by query the active sites, but also predict an unknown protein function, including distant homologous proteins or convergent proteins, by searching to functional active site database. This algorithm also annotates the distant homologous or convergent protein/enzyme active sites.


Assists users in modeling and analyzing protein structures. Jackal provides a collection of programs designed for: (1) comparative modeling based on single, composite or multiple templates; (2) side-chain prediction; (3) modeling residue mutation, insertion or deletion; (4) loop prediction; (5) structure refinement; (6) reconstruction of protein missing atoms; (7) reconstruction of protein missing residues; (8) prediction of hydrogen atoms; (9) fast calculation of solvent accessible surface area; (10) structure superimposition and (11) manipulation of protein structure in torsional angle space.