Prediction of structure from sequence: servers and programs

Finding a model for molecular replacement

• phyre - Protein Homology/analogY Recognition Engine

3D prediction

• SAM_T08 - Kevin Karplus' server tested in CASP7. From the webpage: 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 alpahbets, 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. Look carefully at the E-values for the best hits, as full 3D models are constructed even when the E-values are high (and the resulting models are not then not trustworthy).
• 3Djigsaw - This server builds three-dimensional models for proteins based on homologues of known structure
• Robetta provides both ab initio and comparative models of protein domains. It uses the ROSETTA fragment insertion method (Simons et al. (1997) J Mol Biol. 268:209-225). Domains without a detectable PDB homolog are modeled with the Rosetta de novo protocol (Bonneau et al. (2002) J Mol Biol. 322:65-78).

Protein Model Portal - PSI SGKB

• http://www.proteinmodelportal.org/index.php?pid=tools