current user: public
Important: Please also cite original resources that were used to build FFAS profiles if they were accessed from results of FFAS searches and used in your research.
|FFAS is regularly assessed in CASP and LIVEBENCH experiments. In the last LIVEBENCH evaluation, FFAS ranked at the top of all sequence-based methods. In addition, FFAS is continuously tested with benchmarks consisting of pairs of similar structures derived from the SCOP database. The current version of FFAS algorithm was optimized in 2003 using SCOP v.1.65 and it was retested in 2011 using only superfamilies that were added in later versions of SCOP and, thus, not used in any training set or algorithm optimization. Results of benchmarking of FFAS, PSI-Blast, and Blast: A) benchmark of all SCOP domains clustered at 25% seq. id. B) benchmark of very remote homologs consisting of pairs of domains from the same fold but from different superfamilies.|
All these proteomes were processed as follows:
Signal peptides were predicted with the SignalP program and removed from all sequences. Proteins containing more than 1000 residues were split into overlapping fragments of 500 residues.
Once signed in, all results of the searches performed by the user are automatically stored in her/his account. Results of pairwise alignments are not stored in any results list on the server but can be accessed for three month via their URL.
FFAS is supported by the NIH grant R01-GM087218-01
Selected papers from Godzik Lab|
Ying Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley Deacon, John Wooley, Scott Lesley, Ian Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik. Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima. Science. 2009 Sep 18;325(5947):1544-9.
Mayya Sedova, Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Kai W Post, Thomas Hrabe, Eduard Porta-Pardo, Adam Godzik Cancer3D 2.0:: interactive analysis of 3D patterns of cancer mutations in cancer subsets. Nucleic Acids Research, gky1098 2018; Published on November 8 2018.
Grynberg M, Godzik A. NERD: a DNA processing-related domain present in the anthrax virulence plasmid, pXO1. Trends Biochem Sci. 2004 Mar;29(3):106-10.