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Showing 9 records out of 9 total

Categories: proteomics, (protein structure) - Software type(s): website - tool
CPHmodels 3.2 is a protein homology modeling server. The template recognition is based on profile-profile alignment guided by secondary structure and exposure predictions
Categories: proteomics, (protein structure) - Software type(s): website - tool
ESyPred3D is an automated homology modeling program. The method gets benefit of the increased alignment performances of a new alignment strategy using neural networks. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three dimensional structure is built using the modeling package MODELLER
Categories: proteomics, (protein structure) - Software type(s): website - tool
FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure
Categories: proteomics, (protein structure) - Software type(s): website - tool
Geno3D is an automatic web server for protein molecular modelling
Categories: proteomics, (protein structure) - Software type(s): website - tool
Homology detection & structure prediction by HMM-HMM comparison
Categories: proteomics, (protein structure) - Software type(s): website - tool
As with Phyre, the new system is designed around the idea that you have a protein sequence/gene and want to predict its three-dimensional (3D) structure. Whereas Phyre used a profile-profile alignment algorithm, Phyre2 uses the alignment of hidden Markov models via HHsearch to significantly improve accuracy of alignment and detection rate.
Categories: proteomics, (protein structure) - Software type(s): website - tool
The PSIPRED Protein Structure Prediction Server aggregates several of our structure prediction methods into one location. Users can submit a protein sequence, perform the prediction of their choice and receive the results of the prediction via e-mail.
Categories: proteomics, (protein structure) - Software type(s): website - tool
This server finds similar protein sequences in NR and aligns them, providing sequence logos that show relative conservation of different positions. Local structure predictions are done with neural nets for several different local structure alphabets, and hidden Markov models are created. Fold recognition and alignment to proteins in the Protein Data Bank are done, and a full three-dimensional model is constructed.
Categories: proteomics, (protein structure), structural bioinformatics, biophysics - Software type(s): website - tool
SWISS-MODEL is a fully automated web based protein structure homology-modeling expert system. The SWISS-MODEL Workspace is a web-based integrated service which assist and guides the user in building protein homology models at different levels of complexity. A personal working environment (workspace), where several modelling projects can be carried out in parallel, is provided for each user.