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<h2>References</h2>
<ol>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PredictProtein</font>: </a> <cite>B Rost,G Yachdav and J Liu (2004) The PredictProtein Server. Nucleic Acids Research 32(Web Server issue):W321-W326.
</cite></strong>
<ul>
<li> Author: B Rost
<li> Contact: help@predictprotein.org
<li> URL: <a href="http://www.predictprotein.org">http://www.predictprotein.org</a>
<li> Version: 10.20.04
<li> Description: PredictProtein is the acronym for all prediction programs run.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PROSITE</font>: </a> <cite>A Bairoch, P Bucher ∧ K Hofmann (1997) Nucleic Acids Research, 25:217-221
</cite></strong>
<ul>
<li> Author: A Bairoch, bairoch@cmu.unige.ch P Bucher ∧ K Hofmann
<li> Contact: bairoch@cmu.unige.ch
<li> URL: <a href="http://www.expasy.ch/prosite">http://www.expasy.ch/prosite</a>
<li> Version: 99.07
<li> Description: PROSITE is a database of functional motifs. ScanProsite, finds all functional motifs in your sequence that are annotated in the ProSite db.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">SEG</font>: </a> <cite>J C Wootton ∧ S Federhen (1996) Methods in Enzymology, 266:554-571
</cite></strong>
<ul>
<li> Author: J C Wootton ∧ S Federhen, wootton@ncbi.nlm.nih.gov
<li> Contact: help@predictprotein.org
<li> URL: <a href="wootton@ncbi.nlm.nih.gov">wootton@ncbi.nlm.nih.gov</a>
<li> Version: 1994
<li> Description: SEG divides sequences into regions of low-, and high-complexity. Low-complexity regions typically correspond to 'simple sequences' or 'compositionally-biased' regions.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">ProDom</font>: </a> <cite>ELL Sonnhammer ∧ D Kahn (1994) Protein Science, 3:482-492
</cite></strong>
<ul>
<li> Author: LL Sonnhammer; J Gouzy, F Corpet, F Servant, D Kahn, dkahn@zyx.toulouse.inra.fr
<li> Contact: dkahn@zyx.toulouse.inra.fr
<li> URL: <a href="http://protein.toulouse.inra.fr/prodom.html">http://protein.toulouse.inra.fr/prodom.html</a>
<li> Version: 2000.1
<li> Description: ProDom is a database of putative protein domains. The database is searched with BLAST for domains corresponding to your protein.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PHD</font>: </a> <cite>B Rost (1996) Methods in Enzymology, 266:525-539
</cite></strong>
<ul>
<li> Author: B Rost
<li> Contact: help@predictprotein.org
<li> URL: <a href="http://cubic.bioc.columbia.edu">http://cubic.bioc.columbia.edu</a>
<li> Version: 1.96
<li> Description: PHD is a suite of programs predicting 1D structure (secondary structure, solvent accessibility) from multiple sequence alignments.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PHDsec</font>: </a> <cite>B Rost ∧ C Sander (1993) J. of Molecular Biology, 232:584-599
</cite></strong>
<ul>
<li> Author: B Rost
<li> Contact: help@predictprotein.org
<li> URL: <a href="http://cubic.bioc.columbia.edu">http://cubic.bioc.columbia.edu</a>
<li> Version: 1.96
<li> Description: PHDsec predicts secondary structure from multiple sequence alignments.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PHDacc</font>: </a> <cite>B Rost ∧ C Sander (1994) Proteins, 20:216-226
</cite></strong>
<ul>
<li> Author: B Rost
<li> Contact: help@predictprotein.org
<li> Version: 1.96
<li> Description: PHDacc predicts per residue solvent accessibility from multiple sequence alignments.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PHDhtm</font>: </a> <cite>B Rost, P Fariselli ∧ R Casadio (1996) Protein Science, 7:1704-1718
</cite></strong>
<ul>
<li> Author: B Rost
<li> Contact: help@predictprotein.org
<li> URL: <a href="http://cubic.bioc.columbia.edu">http://cubic.bioc.columbia.edu</a>
<li> Version: 1.96
<li> Description: PHDhtm predicts the location and topology of transmembrane helices from multiple sequence alignments.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PROF</font>: </a> <cite>B Rost (2004) Meth. Mol. Biol., submitted.
</cite></strong>
<ul>
<li> Author: B Rost
<li> Contact: help@predictprotein.org
<li> Version: 2000_04
<li> Description: PROF is a suite of programs predicting 1D structure (secondary structure, solvent accessibility) from multiple sequence alignments.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PROFsec</font>: </a> <cite>B Rost (2004) Meth. Mol. Biol., submitted.
</cite></strong>
<ul>
<li> Author: B Rost
<li> Contact: help@predictprotein.org
<li> URL: <a href="http://cubic.bioc.columbia.edu ">http://cubic.bioc.columbia.edu </a>
<li> Version: 2000_04
<li> Description: PROFsec predicts secondary structure from multiple sequence alignments.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PROFACC</font>: </a> <cite>B Rost (2004) Meth. Mol. Biol., submitted.
</cite></strong>
<ul>
<li> Author: B Rost
<li> Contact: help@predictprotein.org
<li> URL: <a href="http://cubic.bioc.columbia.edu">http://cubic.bioc.columbia.edu</a>
<li> Version: 2000_04
<li> Description: PROFacc predicts per residue solvent accessibility from multiple sequence alignments.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">GLOBE</font>: </a> <cite>B Rost (1998) unpublished
</cite></strong>
<ul>
<li> Author: B Rost
<li> Contact: help@predictprotein.org
<li> URL: <a href="http://cubic.bioc.columbia.edu/papers/1999_globe/paper.html">http://cubic.bioc.columbia.edu/papers/1999_globe/paper.html</a>
<li> Version: 1.98.05
<li> Description: GLOBE predicts the globularity of a protein
</ul>
<!--
<li><a NAME="quote_pp"><strong><font SIZE="+1">CYSPRED</font>: </a> <cite>Fariselli P, Riccobelli P ∧ Casadio R (1999) PROTEINS 36:340-346
</cite></strong>
<ul>
<li> Author: Fariselli P, Riccobelli P, Casadio R
<li> Contact: piero@lipid.biocomp.unibo.it
<li> URL: <a href="http://prion.biocomp.unibo.it/cyspred.html">http://prion.biocomp.unibo.it/cyspred.html</a>
<li> Version: 0
<li> Description: CYSPRED finds whether the cys residue in your protein forms disulfide bridge.
</ul>
-->
<li><a NAME="quote_pp"><strong><font SIZE="+1">DISULFIND</font>: </a> <cite>A.Ceroni, P.Frasconi, A.Passerini and A.Vullo (2004) Bioinformatics, 20, 653-659, 2004
</cite></strong>
<ul>
<li> Author: A.Ceroni, P.Frasconi, A.Passerini and A.Vullo
<li> Contact: cystein@dsi.unifi.it
<li> URL: <a href="http://cassandra.dsi.unifi.it/cysteines/index.html">http://cassandra.dsi.unifi.it/cysteines/index.html</a>
<li> Version: 2.0
<li> Description: DISULFIND is a disulphide bridges predictor based on a two steps process.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">A conformational switch prediction program</font>: </a> <cite>Young et al. Protein Science(1999) 8:1752-64.
</cite></strong>
<ul>
<li> Author: Young M, Kirshenbaum K, Dill KA and Highsmith S.
<li> Contact: mmyoung@sandia.gov, kent@cheme.caltech.edu, shighsmith@sf.uop.edu
<li> Version: 1.0
<li> Description: ASP finds regions that are most likely to behave as switches in proteins known to exhibit this behavior
</ul>
<li> <a NAME="quote_pp"><strong><font SIZE="+1">HMMPFAM:</font></a> <cite>Bateman et al. Nucleic Acids Research 2004 32:D138-D141.</cite></strong>
<ul>
<li> Author: Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR.
<li> Contact: agb@sanger.ac.uk
<li> Version: 2.2g
<li> Description: Search one or more sequences against HMM database
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">DISULFIND</font>: </a> <cite>A.Ceroni, P.Frasconi, A.Passerini and A.Vullo (2004) Bioinformatics, 20, 653-659, 2004
</cite></strong>
<ul>
<li> Author: A.Ceroni, P.Frasconi, A.Passerini and A.Vullo
<li> Contact: cystein@dsi.unifi.it
<li> URL: <a href="http://cassandra.dsi.unifi.it/cysteines/index.html">http://cassandra.dsi.unifi.it/cysteines/index.html</a>
<li> Version: 2.0
<li> Description: DISULFIND is a disulphide bridges predictor based on a two steps process.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">NORS</font>: </a> <cite>Liu J, Rost B (2003) NORSp: predictions of long regions without regular secondary structure. Nucleic Acids Research 31(13):3833-3835
</cite></strong>
<ul>
<li> Author: J. Liu
<li> Contact: Jinfeng Liu <jinfeng.liu@gmail.com>
<li> URL: <a href="http://cubic.bioc.columbia.edu/services/NORSp/">http://cubic.bioc.columbia.edu/services/NORSp/</a>
<li> Version: 1.0
<li> Description: NORSp is a predictor of NOn-Regular Secondary Structure.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">CHOP</font>: </a> <cite>Liu J ∧ Rost B (2004) CHOP proteins into structural domain-like fragments. Proteins, 55(3):678-688
</cite></strong>
<ul>
<li> Author: J. Liu
<li> Contact: Jinfeng Liu <jinfeng.liu@gmail.com>
<li> URL: <a href="http://cubic.bioc.columbia.edu/services/chop/">http://cubic.bioc.columbia.edu/services/chop/</a>
<li> Version: 1.0
<li> Description: CHOP is a method of dissecting proteins into domain-like fragments based on sequence homology.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">ISIS</font>: </a> <cite>Yanay Ofran and Burkhard Rost (2007). ISIS: Interaction Sites Identified from Sequence. Bioinformatics. 23 (2), e13-e16
</cite></strong>
<ul>
<li> Author: Y. Ofran
<li> Contact: Yanay Ofran <yanay@ofranlab.org>
<li> URL: <a href="http://cubic.bioc.columbia.edu/services/isis/index.php">http://cubic.bioc.columbia.edu/services/isis/</a>
<li> Version: 1.0
<li> Description: Prediction of residues involved in external protein-protein interactions.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">DISIS</font>: </a> <cite>Yanay Ofran and Venkatesh Mysore and Burkhard Rost (2007). Prediction of DNA-binding residues from sequence. Bioinformatics. 23 (13), i347-i353
</cite></strong>
<ul>
<li> Author: Y. Ofran
<li> Contact: Yanay Ofran <yanay@ofranlab.org>
<li> URL: <a href="http://cubic.bioc.columbia.edu/services/disis/">http://cubic.bioc.columbia.edu/services/disis/</a>
<li> Version: 1.0
<li> Description: Prediction of residues involved in DNA binding.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">NORSnet</font>: </a> <cite>Avner Schlessinger and Jinfeng Liu and Burkhard Rost (2007). Natively unstructured loops differ from other loops. PLoS Computational Biology. 3 (7), e140.
</cite></strong>
<ul>
<li> Author: A. Schlessinger
<li> Contact: Avner Schlessinger <avnersch@gmail.com>
<li> URL: <a href="http://predictprotein.org/">http://predictprotein.org/</a>
<li> Version: 1.0.4
<li> Description: Identifies unstructured loops from sequence.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PROFbval</font>: </a> <cite>Avner Schlessinger and Guy Yachdav and Burkhard Rost (2006). PROFbval: predict flexible and rigid residues in proteins. Bioinformatics. 22 891-893.</cite></strong>
<ul>
<li> Author: A. Schlessinger
<li> Contact: Avner Schlessinger <avnersch@gmail.com>
<li> URL: <a href="http://cubic.bioc.columbia.edu/newwebsite/services/Profbval">http://cubic.bioc.columbia.edu/newwebsite/services/Profbval</a>
<li> Version: 1.0.4
<li> Description: Prediction of protein flexibility and rigidity prediction from sequence.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">METADISORDER</font>: </a> <cite>A. Schlessinger and M. Punta and G. Yachdav and L. Kajan and B. Rost (2009). Improved disorder prediction by combination of orthogonal approaches. PLoS One. 4 (2), e4433.</cite></strong>
<ul>
<li> Author: A. Schlessinger
<li> Contact: Avner Schlessinger <avnersch@gmail.com>
<li> URL: <a href="http://cubic.bioc.columbia.edu/newwebsite/services/md/">http://cubic.bioc.columbia.edu/newwebsite/services/md/index.php</a>
<li> Version: 1.0.3
<li> Description: Protein disorder prediction based on orthogonal sources of information.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PROFcon</font>: </a> <cite>Marco Punta and Burkhard Rost (2005). PROFcon: novel prediction of long-range contacts. Bioinformatics. 21 (13), 2960-2968</cite></strong>
<ul>
<li> Author: M. Punta
<li> Contact: Marco Punta <punta@rostlab.org>
<li> URL: <a href=http://cubic.bioc.columbia.edu/services/profcon/">http://cubic.bioc.columbia.edu/services/profcon/</a>
<li> Version: 1.0
<li> Description: contact prediction method.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">PROFtmb</font>: </a> <cite>Henry Bigelow and Burkhard Rost (2006). PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Research. 34 (Web Server issue), W186-188.</cite></strong>
<ul>
<li> Author: H. Bigelow
<li> Contact: Henry Bigelow <hrbigelow@gmail.com>
<li> URL: <a href=http://cubic.bioc.columbia.edu/services/proftmb/">http://cubic.bioc.columbia.edu/services/proftmb/</a>
<li> Version: 1.1.1
<li> Description: per-residue prediction of bacterial transmembrane beta barrels.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">SNAP</font>: </a> <cite>Yana Bromberg and Guy Yachdav and Burkhard Rost (2008). SNAP predicts effect of mutations on protein function. Bioinformatics. in press.</cite></strong>
<ul>
<li> Author: Y. Bromberg
<li> Contact: Yana Bromberg <bromberg@rostlab.org>
<li> URL: <a href=http://cubic.bioc.columbia.edu/services/snap/">http://cubic.bioc.columbia.edu/services/snap/</a>
<li> Version: 1.0.8
<li> Description: a method for evaluating effects of single amino acid substitutions on protein function.
</ul>
<li><a NAME="quote_pp"><strong><font SIZE="+1">LOCtree</font>: </a> <cite>Rajesh Nair and Burkhard Rost (2005). Mimicking cellular sorting improves prediction of subcellular localization. Journal of Molecular Biology. 348 (1), 85-100</cite></strong>
<ul>
<li> Author: R. Nair
<li> Contact: Rajesh Nair <rajnair5@gmail.com>
<li> URL: <a href=http://cubic.bioc.columbia.edu/services/loctree/">http://cubic.bioc.columbia.edu/services/loctree/</a>
<li> Version: 1.0.3
<li> Description: predict the subcellular localization of proteins.
</ul>
</ol>
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