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--- pspp [2009/11/23 09:05] – 172.26.0.166
+++ pspp [2010/05/22 14:19] (current) – external edit 127.0.0.1
@@ Line 2: / Line 2: @@
 Protein structures are critical for understanding the mechanisms of biological systems and, subsequently, for drug and vaccine design. Unfortunately, protein sequence data exceed structural data by a factor of more than 200 to 1. This gap can be partially filled by using computational protein structure prediction. While structure prediction Web servers are a notable option, they often restrict the number of sequence queries and/or provide a limited set of prediction methodologies. Therefore, we present a standalone protein structure prediction software package suitable for high-throughput structural genomic applications that performs all three classes of prediction methodologies: comparative modeling, fold recognition, and ab initio. This software can be deployed on a user's own high-performance computing cluster.
-[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0006254;jsessionid=FAFDBB60D6EF54E714F6B66FFF8B0FF7]]
+[[http://ukpmc.ac.uk/articlerender.cgi?tool=pubmed&pubmedid=19606223]]
 DISPRO/SSPRO
@@ Line 29: / Line 29: @@
 Running FIEFDom
 <code>FIEFDom<WIN/LIN>.exe <input.fasta></code>
+Rosetta and PyRosetta Software
+Rosetta Software Logo from Baker Laboratory
+Rosetta is a molecular modeling software package for understanding protein structures, protein design, protein docking, protein-DNA and protein-protein interactions. The Rosetta software contains multiple functional modules, including Rosetta ab initio, RosettaNMR, RosettaDesign, RosettaDock, Rosetta Fragment Selection, Rosetta Nucleic Acids, RosettaLigand, and more.
+./prospect_ssp.LINUX -prospect_path /home/magochi/src/PSPP/pspp_1.0/prospect/prospect -seqfile /home/magochi/seq.fasta