FFAS03: a server for profile–profile sequence alignments

By Lukasz Jaroszewski, Leszek Rychlewski, Jim Zhanwen Li, Weizhong Li, Adam Godzik. 2005

571 citations recorded by the source corpus.

The FFAS03 server provides a web interface to the third generation of the profile–profile alignment and fold-recognition algorithm of fold and function assignment system (FFAS) [L. Rychlewski, L. Jaroszewski, W. Li and A. Godzik (2000), Protein Sci., 9, 232–241]. Profile–profile algorithms use information present in sequences of homologous proteins to amplify the patterns defining the family. As a result, they enable detection of remote homologies beyond the reach of other methods. FFAS, initially developed in 2000, is consistently one of the best ranked fold prediction methods in the CAFASP and LiveBench competitions. It is also used by several fold-recognition consensus methods and meta-servers. The FFAS03 server accepts a user supplied protein sequence and automatically generates a profile, which is then compared with several sets of sequence profiles of proteins from PDB, COG, PFAM and SCOP. The profile databases used by the server are automatically updated with the latest structural and sequence information. The server provides access to the alignment analysis, multiple alignment, and comparative modeling tools. Access to the server is open for both academic and commercial researchers. The FFAS03 server is available at .

Subfields: Materials Chemistry, Molecular Biology

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In Materials Chemistry

1. Ben M. Webb
2. Yang Zhang
3. Jinbo Xu
4. Andrej Sali
5. Sheng Wang
6. Jianzhu Ma
7. Randy J. Read
8. Min-Yi Shen

In Molecular Biology

1. Jinbo Xu
2. Yang Zhang
3. Ben M. Webb
4. Andrej Sali
5. Sheng Wang
6. Jianzhu Ma
7. Jianlin Cheng
8. Torsten Schwede

Citations in the corpus

• Improvement of molecular-replacement models with Sculptor (2011, methodology): “For certain models, FFAS (Jaroszewski et al., 2005) alignments were also used for comparison with other alignments.”
• LOMETS: A local meta-threading-server for protein structure prediction (2007, methodology): “In the 3D-Jury meta-server, for example, there was only one server from FFAS03 (9) that was available during the CASP7 season.”
• Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains (2016, background): “For PH-like domains in yeast, InterPro provides useful data, but its output is not close to 100% sensitive, only including 61 of 73 domains (Table S2).(47,48) Also, it is not entirely specific, as it includes 3 false positives (Table S2).”
• Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives (2012, methodology): “SAM[31],HMMER[32] or profileprofile alignment such as FFAS03[33], profilescan[34] and HHsearch.”
• Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre (2008, background): “11–14 All these methods have their strengths and weaknesses.”
• MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins (2012, methodology): “…database local installation [37] FFAS Profile-profile alignment and fold-recognition algorithm for fold and function assignment local installation [35] mGenThreader The method combines profile-profile alignments with secondary-structure specific gap-penalties, classic pair-and solvation…”
• Comparative Protein Structure Modeling Using MODELLER (2007, unknown): “Some of the programs that can be used to detect suitable templates are FFAS (Jaroszewski et al., 2005), SP3 (Zhou and Zhou, 2005), SALIGN (Marti-Renom et al., 2004), and PPSCAN (Eswar et al., 2005).”
• MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information (2008, methodology): “4–6 There have been a number of threading algorithms in literature based on various approaches, for example the sequence profile–profile alignment,7–14 structural profile alignment,15–17 hidden Markov models,18–20 machine learning,21,22 and pair-wise potentials with optimal searching.”
• Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome (2010, unknown): “Models resulting from FFAS (34) hits to 2g0u chain A and 2jow were refined using Modeler (35), resulting in confident structure predictions for residues 23–98of PrgJ.”
• MrGrid: A Portable Grid Based Molecular Replacement Pipeline (2010, unknown): “Second, the emergence of more sophisticated sequence searching algorithms, such as profile-profile matching [2], improve the probability of finding a suitable search model, even in cases of very low similarity (,20% identity).”