Nucleic Acids Research

Nucleic Acids Research 2004 32(Web Server Issue):W321-W326; doi:10.1093/nar/gkh377

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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

The PredictProtein server

Burkhard Rost^1,2,3,*, Guy Yachdav^1,3 and Jinfeng Liu^1,2

¹ CUBIC and ² North East Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA and ³ Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, 1150 St Nicholas Avenue, New York, NY 10032, USA

^* To whom correspondence should be addressed. Tel: +1 212 305 4018; Fax: +1 212 305 7932; Email: rost{at}columbia.edu

Received February 13, 2004; Revised and Accepted March 15, 2004

PredictProtein (http://www.predictprotein.org) is an Internet service for sequence analysis and the prediction of protein structure and function. Users submit protein sequences or alignments; PredictProtein returns multiple sequence alignments, PROSITE sequence motifs, low-complexity regions (SEG), nuclear localization signals, regions lacking regular structure (NORS) and predictions of secondary structure, solvent accessibility, globular regions, transmembrane helices, coiled-coil regions, structural switch regions, disulfide-bonds, sub-cellular localization and functional annotations. Upon request fold recognition by prediction-based threading, CHOP domain assignments, predictions of transmembrane strands and inter-residue contacts are also available. For all services, users can submit their query either by electronic mail or interactively via the World Wide Web.

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The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.

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				S. Kolkenbrock, K. Parschat, B. Beermann, H.-J. Hinz, and S. Fetzner N-Acetylanthranilate Amidase from Arthrobacter nitroguajacolicus Ru61a, an {alpha}/{beta}-Hydrolase-Fold Protein Active towards Aryl-Acylamides and -Esters, and Properties of Its Cysteine-Deficient Variant J. Bacteriol., December 15, 2006; 188(24): 8430 - 8440. [Abstract] [Full Text] [PDF]

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				A. A. Nuara, H. Bai, N. Chen, R. M. L. Buller, and M. R. Walter The Unique C Termini of Orthopoxvirus Gamma Interferon Binding Proteins Are Essential for Ligand Binding J. Virol., November 1, 2006; 80(21): 10675 - 10682. [Abstract] [Full Text] [PDF]

				Y.-G. Kim, H.-J. Park, K. K. Kim, K. Lowenhaupt, and A. Rich A peptide with alternating lysines can act as a highly specific Z-DNA binding domain Nucleic Acids Res., October 18, 2006; 34(17): 4937 - 4942. [Abstract] [Full Text] [PDF]

				S. Archak and J. Nagaraju Eicosapentapeptide repeats (EPRs): novel repeat proteins specific to flowering plants Bioinformatics, October 15, 2006; 22(20): 2455 - 2458. [Abstract] [Full Text] [PDF]

				D. P. Terwilliger, K. M. Buckley, D. Mehta, P. G. Moorjani, and L.C. Smith Unexpected diversity displayed in cDNAs expressed by the immune cells of the purple sea urchin, Strongylocentrotus purpuratus Physiol Genomics, September 14, 2006; 26(2): 134 - 144. [Abstract] [Full Text] [PDF]

				D. Cordella, M. Muzza, L. Alberti, P. Colombo, P. Travaglini, P. Beck-Peccoz, L. Fugazzola, and L. Persani An in-frame complex germline mutation in the juxtamembrane intracellular domain causing RET activation in familial medullary thyroid carcinoma. Endocr. Relat. Cancer, September 1, 2006; 13(3): 945 - 953. [Abstract] [Full Text] [PDF]

				M. Fujiki, S. Kawakami, R. W. Kim, and R. N. Beachy Domains of tobacco mosaic virus movement protein essential for its membrane association J. Gen. Virol., September 1, 2006; 87(9): 2699 - 2707. [Abstract] [Full Text] [PDF]

				H. Matsumura, K. Izui, and K. Mizuguchi A novel mechanism of allosteric regulation of archaeal phosphoenolpyruvate carboxylase: a combined approach to structure-based alignment and model assessment Protein Eng. Des. Sel., September 1, 2006; 19(9): 409 - 419. [Abstract] [Full Text] [PDF]

				N. C. K. Heng, N. L. Ragland, P. M. Swe, H. J. Baird, M. A. Inglis, J. R. Tagg, and R. W. Jack Dysgalacticin: a novel, plasmid-encoded antimicrobial protein (bacteriocin) produced by Streptococcus dysgalactiae subsp. equisimilis Microbiology, July 1, 2006; 152(7): 1991 - 2001. [Abstract] [Full Text] [PDF]

				A. Ceroni, A. Passerini, A. Vullo, and P. Frasconi DISULFIND: a disulfide bonding state and cysteine connectivity prediction server. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W177 - W181. [Abstract] [Full Text] [PDF]

				S. Sharma, S. L. Ang, M. Shaw, D. A. Mackey, J. Gecz, J. W. McAvoy, and J. E. Craig Nance-Horan syndrome protein, NHS, associates with epithelial cell junctions Hum. Mol. Genet., June 15, 2006; 15(12): 1972 - 1983. [Abstract] [Full Text] [PDF]

				P. G. Dunton, W. J. Mawby, V. A. Shaw, and A. E. Walsby Analysis of tryptic digests indicates regions of GvpC that bind to gas vesicles of Anabaena flos-aquae Microbiology, June 1, 2006; 152(6): 1661 - 1669. [Abstract] [Full Text] [PDF]

				P. G. Ulery, G. Rudenko, and E. J. Nestler Regulation of {Delta}FosB Stability by Phosphorylation. J. Neurosci., May 10, 2006; 26(19): 5131 - 5142. [Abstract] [Full Text] [PDF]

				A. Obarska, A. Blundell, M. Feder, S. Vejsadova, E. Sisakova, M. Weiserova, J. M. Bujnicki, and K. Firman Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA Nucleic Acids Res., April 13, 2006; 34(7): 1992 - 2005. [Abstract] [Full Text] [PDF]

				N. Dubarry, F. Pasta, and D. Lane ParABS Systems of the Four Replicons of Burkholderia cenocepacia: New Chromosome Centromeres Confer Partition Specificity J. Bacteriol., February 15, 2006; 188(4): 1489 - 1496. [Abstract] [Full Text] [PDF]

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