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PP Help 02: Quote and copyright

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QUOTE and COPYRIGHT

Who are we?

Current team:
- Burkhard Rost (CUBIC, Columbia Univ, New York / LION, Heidelberg WWW, rost@columbia.edu ) pioneered the PredictProtein service; wrote the PHD prediction programs: PHDsec, PHDacc, PHDhtm, and PHDtopology; developed the prediction-based threading method PHDthreader/TOPITS; programmed, and proposed the scores compiled by EvalSec; hacked some of the PredictProtein scripts; is helping to keep the service up and running, and is responsible for the documentation.
- Volker Eyrich (Chemistry Dept, Columbia Univ, New York, volker@chem.columbia.edu ) wrote the scripts for the META server which allows you to access a large variety of selected servers world-wide from a single-page interface.
- Jinfeng Liu (CUBIC, Columbia Univ, New York WWW, liu@cubic.bioc.columbia.edu ) is currently maintaining the PredictProtein server.
Others who contributed (in the past):
- Reinhard Schneider (now LION, Heidelberg, , WWW, schneider@lion-ag.de) wrote the program MaxHom for multiple sequence, and 1D structure alignments, and helped the service take off.
- Antoine de Daruvar (now Univ. Bordeaux and LION, Heidelberg) rewrote the scripts managing requests, and maintained the service running for twelve months.
- Chris Sander (now Millennium, Boston, sander@mpi.com) organised resources, contributed ideas, and simulated the grand guru.
People running PP mirrors:
1. Shoba Ranganathan (ANGIS centre, Sydney University, Australia shoba@angis.org.au) made sure the first mirror of PP came from down-under .. (mirror).
2. Betty Cheng (BIC, BioInformatics Centre, National Univ of Singapore, betty@bic.nus.edu.sg) made sure the second mirror would also reside far enough away .. (mirror)
3. Jose Valverde (CNB National Centre of Biotechnology, Madrid, Spain, jrvalverde@cnb.uam.es) maintains the first Mediterranean mirror (mirror).
4. Kunchur Gururprasad (CDFD, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India , guru@www.cdfd.org.in ) maintains the first mirror in India (mirror).
5. Manuela Helmer-Citterich (University 'Tor Vergata', Rome, Italy, citterich@uniroma2.it) maintains the mirror in Italy (mirror).
6. Sunita Jagtap (Bioinformatics Centre, University of Pune, India , sunita@bioinfo.ernet.in) maintains the second mirror in India (mirror).
7. Daniel Fischer (Univ Ben Gurion, Beer-Sheva, Israel, dfischer@cs.bgu.ac.il) maintains the mirror in Israel (mirror).
8. Torsten Schwede (Biocentre, Basel, Switzerland, torsten.schwede@unibas.ch) maintains the mirror at the Biocentre in Basel (mirror).
9. Jack Leunissen (CMBI Centre, University Nijmegen, The Netherlands , jackl@caos.kun.nl) maintains the mirror in the Netherlands (mirror).
10. Dmitry Rykunov (Inst for protein research (RAS), Pushchino, Russa, rykunov@antares.protres.ru ) maintains the mirror in first Eastern European mirror in Russia (mirror). Although Dmitry was the twelfth to install a mirror, he was the first who unearthed a bunch of broken links on the PP web pages!
11. Phil Bourne (San Diego Supercomputer Center, USA, bourne@sdsc.edu ) maintains the first US mirror with a fast connection in San Diego (mirror).
12. Lorenzo Segovia (UNAM Cuernavaca, Mexico lorenzo@ibt.unam.mx ) maintains the first Latin American mirror in Mexico (mirror).
13. Bahram Goliaei (IBC Tehran, Iran goliaei@ibc.ut.ac.ir ) maintains the first mirror in Iran (mirror).
14. Gang Fang (CBI Peking, China fangg@lsc.pku.edu.cn ) maintains the first mirror in China (mirror).
15. Juncai Ma (Inst. Microbiol., China ma@sun.im.ac.cn ) maintains a mirror in Chinese Academy of Science (mirror).
Authors of other programs used:
- Stephen F Altschul and Samuel Karlin (NCBI, WWW, altschul@ncbi.nlm.nih.gov) wrote the initial database search bestseller BLAST.
- Stephen F Altschul and colleagues (NCBI, WWW, altschul@ncbi.nlm.nih.gov) wrote the recent hit PSI-BLAST.
- Amos Bairoch (Geneva, WWW, bairoch@cmu.unige.ch) maintains SWISS-PROT, and initialised ProSite (as well as, numerous other services!).
- Amos Bairoch, Philip Bucher, Kay Hofmann (Geneva, WWW, bairoch@cmu.unige.ch) maintain ProSite, and wrote the scripts returning the ProSite output.
- Nigel Brown (London, WWW, <nbrown@nimr.mrc.ac.uk) has developed the program MView which is a rather powerful tool for automatically displaying alignments.
- Florence Corpet, Jerome Gouzy & Daniel Kahn (Toulouse, WWW, dkahn@zyx.toulouse.inra.fr) maintain the ProDom database of domain assignments to all proteins in SWISS-PROT.
- Piero Fariselli (farisel@kaiser.alma.unibo.it) and Rita Casadio (Univ of Bologna, Italy) wrote the program CYSPRED that predicts the disulfide-bonding state of cysteine residues.
- Patrice Gouet (gouet@ipbs.fr) (IPBS, WWW, ) wrote the program ESPript that converts alignments into PostScript, GIF, and TIFF formatted images. Emmanuel Courcelle (manu@ipbs.fr) installed (and maintains) the local mirror of ESPript in New York.
- Andrei Lupas (SmithKline Beecham, Collegeville; lupasa00@mh.us.sbphrd.com) wrote the program COILS (detection of coiled-coil regions).
  Note: the latest version of the source code was provided by Rob Russell (EMBL rob.russell@embl-heidelberg.de).
- Reinhard Schneider (LION, Heidelberg, WWW, email ) wrote the program MaxHom (multiple sequence alignment).
- John C Wootton and Scott Federhen (NCBI, WWW, federhen@ncbi.nlm.nih.gov) wrote the classic program for detecting regions of low-complexity (composition bias).
- Malin M Young(Sandia National Lab, mmyoung@sandia.gov), Kent Kirshenbaum, Ken Dill, and Stefan Highsmith wrote the program for detecting regions likely to undergo structural switches (ASP).
Authors of services available through META:
- SignalP prediction of presence and location of signal peptide cleavage sites in amino acid sequences from different organisms
  Henrik Nielsen, Soeren Brunak (both CBS Copenhagen), and Gunnar von Heijne (Univ Stockholm, Sweden); Administrator: Kristoffer Rapacki rapacki@cbs.dtu.dk
- NetOglyc prediction of mucin type GalNAc O-glycosylation sites in mammalian proteins.
  Jan Hansen (CBS, Copenhagen, Denmark); Administrator: Kristoffer Rapacki rapacki@cbs.dtu.dk
- NetPicoRNA predictions of cleavage sites of picornaviral proteases.
  Nikolaj Blom (CBS, Copenhagen, Denmark); Administrator: Kristoffer Rapacki rapacki@cbs.dtu.dk
- ChloroP predictions of whether or not a protein contains an N-terminal chloroplast transit peptide, cTP, and of probable sites for cleavage of the transit peptide.
  Olof Emanuelsson (CBS Copenhagen, Denmark); Administrator: Kristoffer Rapacki rapacki@cbs.dtu.dk
- JPRED consensus method for protein secondary structure prediction.
  James Cuff, and Geoff Barton (both EBI Hinxton, England); Administrator: James Cuffjames@ebi.ac.uk
- TMHMM prediction of the location of transmembrane helices and their topology.
  Anders Krogh (CBS, Copenhagen, Denmark); Administrator: Anders Krogh krogh@cbs.dtu.dk
- TOPPRED prediction of location and orientation of transmembrane helices.
  Erik Wallin, and Gunnar von Heijne (both Stockholm Univ, Sweden); Administrator: Erik Wallin erikw@biokemi.su.se
- DAS prediction of location of transmembrane helices.
  Miklos Cserzo, Istvan Simon (both Academy of Sciences, Budapest, Hungary), Erik Wallin, Gunnar von Heijne, Arne Elofsson (Stockholm Univ, Sweden); Administrator: Miklos Cserzo miklos@pugh.bip.bham.ac.uk
- FRSVR prediction-based threading, also incorporating purely sequence-based database searches.
  Daniel Fischer (Ben Gurion Univ of the Negev, Israel); Administrator: Daniel Fischer dfischer@cs.bgu.ac.il
- SAMT98 hidden Markov model method (SAM-T98) for finding remote homologs of protein sequences.
  Kevin Karplus, Christian Barrett, and Richard Hughey (all UCSD, Santa Cruz, USA); Administrator: sam-info@cse.ucsc.edu
- SWISS-MODEL prediction of 3D structure by homology modelling (automated server).
  Manuel Peitsch, Torsten Schwede, and Nicolas Guex (all Glaxo, Geneva, Switzerland); Administrator: Nicolas Guex ng45767@GlaxoWellcome.co.uk
- CPHmodels prediction of 3D structure by homology modelling through a collection of methods and databases developed to predict protein structures.
  Ole Lund (CBS, Copenhagen, Denmark); Administrator: Kristoffer Rapacki rapacki@cbs.dtu.dk

Pleeeaze cite for PredictProtein (!!)

Comment: if you find the following list too long, please note that PredictProtein combines a large number of independent tools. Where other servers adopt the philosophy 'one mail/WWW interface per tool' ( for a few examples), PP attempts to provide one single interface to many tools. Many of the tools are at the forefront of bio-informatics (academics may 'pay' these services by quoting).
Links to more literature related to PP.

For general reference to the PredictProtein server:
1. PP: B Rost: PHD: predicting one-dimensional protein structure by profile based neural networks. Meth. in Enzym., 1996, 266, 525-539.(Full paper)
Profile network prediction of secondary structure (PHDsec):
1. PHDsec: B Rost & C Sander: Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 1993, 232, 584-599.
2. PHDsec: B Rost & C Sander: Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 1994, 19, 55-77.
Profile network prediction of solvent accessibility (PHDacc):
1. PHDacc: B Rost & C Sander: Conservation and prediction of solvent accessibility in protein families. Proteins, 1994, 20, 216-226.
Profile network prediction of transmembrane helices (PHDhtm):
1. PHDhtm: B Rost, P Fariselli & R Casadio: Topology prediction for helical transmembrane proteins at 86% accuracy. Prot. Science, 1996, 7, 1704-1718. (Abstract)
Coiled-coil prediction (COILS):
1. COILS: A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 1996, 266, 513-525
Cysteine bond prediction (CYSPRED):
1. CYSPRED: P Fariselli, P Riccobelli & R Casadio: Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins. Proteins, 1999, 36, 340-346.
Structural switching regions (ASP):
1. ASP: MM Young, K Kirshenbaum, KA Dill & S Highsmith: Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64.
Prediction-based threading (TOPITS):
1. TOPITS: B Rost: TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures. In: C Rawlings, D Clark, R Altman, L Hunter, T Lengauer & S Wodak (eds.) "The third international conference on Intelligent Systems for Molecular Biology (ISMB)", Cambridge, U.K., Jul 16-19, 1995, Menlo Park, CA: AAAI Press, 1995, 314-321.
Multiple sequence alignment (MaxHom, HSSP):
1. MaxHom: C Sander; R Schneider: Database of Homology-Derived Structures and the Structural Meaning of Sequence Alignment. Proteins, 1991, 9, 56-68.
2. BLAST: S Karlin & SF Altschul: Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl. Acad. Sci. USA, 1993, 90, 5873-5877.
HTML display of alignments (MView):
1. Mview: N P Brown, C Leroy, C Sander: MView: A Web compatible database search or multiple alignment viewer. Bioinformatics, 1998, 14, 380-381.
PostScript display of alignments (ESPript):
1. ESPript: P Gouet, E Courcelle, D I Stuart & F Metoz: ESPript: multiple sequence alignments in PostScript. Bioinformatics, 15, 305-308, 1999.
Functional sequence motifs (ProSite):
1. ProSite: A Bairoch, P Bucher & K Hofmann: The ProSite database, its status in 1997. Nucl. Acids Res., 1997, 25, 217-221.
Low-complexity regions (SEG):
1. SEG: J C Wootton & S Federhen: Analysis of compositionally biased regions in sequence databases. Methods in Enzymology, 1996, 266, 554-571.
Domain assignments (ProDom):
1. ProDom: F Corpet, J Gouzy, D Kahn: The ProDom database of protein domain families. Nucl. Acids Res, 1998, 26, 323-326.
Evaluation of secondary structure prediction accuracy (EVALSEC):
1. Evalsec: B Rost; C Sander & R Schneider: Redefining the goals of protein secondary structure prediction. J. Mol. Biol., 1994, 235, 13-26.

Please cite for META-PP

Comment: all links to the META services (and the respective publications are in:
cubic.bioc.columbia.edu/predictprotein/doc/explain_meta.html

Copyright

Contact
by fax via:     Predict-Help at +1-212-305 7932
by email via:   predict_help@columbia.edu
or via WWW:     http://cubic.bioc.columbia.edu/predictprotein/send_license.html

Feedback

Address questions, suggestions, bug reports, or comments

by fax via:     Predict-Help at +1-212-305-7932
by email via:   predict_help@columbia.edu
or via WWW:     http://cubic.bioc.columbia.edu/predictprotein/send_feedback.html

Protection of sequence data

Your sequence data is deposited in files to which only the PP administrator (BR) has read access. No one else inside or outside of CUBIC (Columbia University BioInformatics Centre) can read your data, except our system administrators who are held to the highest standards of confidentiality. Occasionally, the PP administrator may look at the data in order to assess the performance of the server.

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