FFAS - A new, updated and maintained version of the Fold & Function Assignment System (FFAS). The FFAS fold assignment method is based on the profile-profile matching algorithm. The crucial part of the algorithm is the novel, two dimensional weighting scheme which takes into account the topology of the evolutionary tree of all the proteins in the homologous family.
Reference - Jaroszewski, L., Rychlewski, L., Li, Z., Li, W. & Godzik, A. (2005) FFAS03: a server for profile-profile sequence alignments. Nucl. Acids Res. 33, W284-W288; Rychlewski, L., Jaroszewski, L., Li, W. & Godzik, A. (2000). Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Science 9, 232-241; Jaroszewski, L., Rychlewski, L. & Godzik, A. (2000). Improving the quality of twilight-zone alignments. Protein Science 9, 1487-1496 ;
Reference - Lukasz Jaroszewski, Weizhong Li and Adam Godzik (2002). In Search for more accurate alignment in the twilight zone. Protein Science 11, 1702-1713
Modeller - MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.
Reference - M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.; A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.; A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.;
SCWRL - SCWRL is a program for prediction of protein side-chain conformations.
Reference - A. A. Canutescu, A. A. Shelenkov, and R. L. Dunbrack, Jr. A graph theory algorithm for protein side-chain prediction. Protein Science 12, 2001-2014 (2003).