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Structure homology search software tools | Protein structure data analysis

Homology modeling aims to build three-dimensional protein structure models using experimentally determined structures of related family members as templates It is currently the most accurate computational method to generate reliable structural…
HOMCOS
Web

HOMCOS HOMology modeling of COmplex Structure

Searches and models the 3D complexes for all molecules in the Protein Data Bank…

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…

PRIMO
Web

PRIMO PRotein Interactive MOdeling

A pipeline for homology modeling of protein monomers. PRIMO is a web interface…

A pipeline for homology modeling of protein monomers. PRIMO is a web interface fully automated for modeling protein targets of interest. The PRIMO interface has been designed to guide users through…

HHPred
Web
Desktop

HHPred

Aims to fill the gap between the fast and widely used homology search programs,…

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…

LRFragLib
Desktop

LRFragLib Logistic Regression based Fragment Library

A fragment-library-construction algorithm. LRFragLib improves the detection of…

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…

SSEalign
Web

SSEalign Secondary Structure Element alignment

Allows homology identification of hypothetical proteins. SSEalign is a…

Allows homology identification of hypothetical proteins. SSEalign is a web-server that can be useful for re-annotating proteins with unknown functions, especially for the bacterial proteins.

ORION
Web
Desktop

ORION Optimized protein fold RecognitION

A web app for homology detection and template-based modeling. ORION relies on a…

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…

GENO3D
Web

GENO3D

A 3D construction based on homology between proteins, geometrical restraints,…

A 3D construction based on homology between proteins, geometrical restraints, and a distance approach. Geno3D is an automatic web server developed to study distance geometry for protein modelling to…

CMASA
Desktop

CMASA Contact MAtrix based local Structural Alignment algorithm

Detects local protein structural similarity. CMASA is an accurate and sensitive…

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…

MaxMod
Desktop

MaxMod

A standalone graphical user interface (GUI) of the MODELLER program which…

A standalone graphical user interface (GUI) of the MODELLER program which combines profile Hidden Markov Model (profile HMM) method with Clustal Omega for the construction of protein homology models.…

PMP
Dataset

PMP Protein Model Portal

Combines structural coverage leveraged from homology models and experimental…

Combines structural coverage leveraged from homology models and experimental protein structures. PMP uses a 3D molecular models in biomedical research to find both experimental structures and…

ESyPred3D
Web

ESyPred3D

An automated homology modeling program. The method gets benefit of the…

An automated homology modeling program. The method gets benefit of the increased alignment performances of a new alignment strategy. Alignments are obtained by combining, weighting and screening the…

MHOLline
Web

MHOLline

Automates protein structure prediction and function annotation. MHOLline…

Automates protein structure prediction and function annotation. MHOLline recognizes and utilizes information of protein sequences including in large-scale genome annotation projects. It is based on…

MINT
Desktop

MINT

Allows basic homology modeling functions of Modeller. MINT is a graphical…

Allows basic homology modeling functions of Modeller. MINT is a graphical implementation of the Modeller software. It permits users to input the name of a sequence file, the Protein Data Bank (PDB)…

BioLuminate
Desktop

BioLuminate

Provides a comprehensive modeling solution for biologics. BioLuminate is a user…

Provides a comprehensive modeling solution for biologics. BioLuminate is a user interface and the kynchpin product of the Biologics Suite that is designed from the ground up, with significant user…

TabSearch
Web

TabSearch

Allows users to detect similarities between tableaux of proteins. TabSearch…

Allows users to detect similarities between tableaux of proteins. TabSearch searches for similar folding patterns from about 75000 entries from ASTRAL SCOP database. The software permits to identify…

ICM
Algorithm

ICM Internal Coordinate Modeling

Allows users to resolve problems bound to structure prediction of peptides,…

Allows users to resolve problems bound to structure prediction of peptides, molecular modeling and design. ICM is a complete internal coordinate system useful for treatment of bond angle and phase…

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