Most Popular Homology Modeling Servers
The following is a list of the 27 most popular homology servers, according to Google PageRank .
PageRank 6:
CE – Combinatorial Extension (CE) Method
CPHmodels – Based on profile-profile alignment guided by secondary structure and exposure predictions
SSM – Secondary Structure Matching is an interactive service for comparing protein structures in 3D
SWISS-MODEL – Automated protein structure homology-modeling server
Vast – NCBI’s structure-structure similarity search service
PageRank 5:
BioInfoBank Meta Server – Protein structure and function prediction methods
Dali – Network service for comparing protein structures in 3D
DejaVu – Input to the server is a pdb file with a secondary structure motif
EsyPred3D – Automated homology modeling program
FATCAT – Approach for flexible protein structure comparison
GENO3D – Automatic modeling of protein 3D structure
HHpred – Homology detection & structure prediction by HMM-HMM comparison
HMMSTR – Ab initio prediction of protein structure from sequence
Modeller – homology or comparative modeling of protein three-dimensional structures
Phyre - Protein Homology/analogY Recognition Engine
Rankprop – Ranking algorithm that exploits the global network structure of similarity relationships among proteins in a database
SAM – HMM-based Protein Structure Prediction
TCoffee – Collection of tools for Computing, Evaluating and Manipulating Multiple
THREADER – Protein fold recognition
SWEET – Constructs 3D models of saccharides from their sequences using standard nomenclature.
PageRank 4:
3d-JIGSAW – Automated system to build three-dimensional models for proteins based on homologues of known structure
Consensus Server – Comparative Modeling
FUGUE – Sequence structure homology recognition
HOMCOS – HOmology Modeling of protein COmplex Structure
Promals3D – Alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.
PageRank 3:
What If – PDB file to be used as template, and the aligned sequences of the template and the model.
SDSC1 is currently not operating, but may be in the future
Note: I came across this interesting article comparing the VAST, CE, DALI, DEJAVU and SSM servers.