Bioinformatics Vol. 19 no. 12 2003
Pages 1589-1591
© 2003 Oxford University Press
Applications Note |
PISCES: a protein sequence culling server
Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
Received on October 4, 2002
; revised on January 30, 2003
; accepted on March 18, 2003
Summary: PISCES is a public server for culling sets of protein sequences from the Protein Data Bank (PDB) by sequence identity and structural quality criteria. PISCES can provide lists culled from the entire PDB or from lists of PDB entries or chains provided by the user. The sequence identities are obtained from PSI-BLAST alignments with position-specific substitution matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists than servers that use BLAST, which is unable to identify many relationships below 40% sequence identity and often overestimates sequence identity by aligning only well-conserved fragments. PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output.
Availability: The server is located at http://www.fccc.edu/research/labs/dunbrack/pisces
Contact: rl_dunbrack{at}fccc.edu
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Duan, M. Huang, C. Ma, L. Li, and Y. Zhou Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures Protein Sci., September 1, 2008; 17(9): 1505 - 1512. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. L. Perskie, T. O. Street, and G. D. Rose Structures, basins, and energies: A deconstruction of the Protein Coil Library Protein Sci., July 1, 2008; 17(7): 1151 - 1161. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. C. Li, D. Bu, X. Gao, J. Xu, and M. Li Designing succinct structural alphabets Bioinformatics, July 1, 2008; 24(13): i182 - i189. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Kron, S. Cichanowicz, A. Hendrick, A. Liu, J. Leykam, and L. A. Kuhn Using structural analysis to generate parasite-selective monoclonal antibodies Protein Sci., June 1, 2008; 17(6): 983 - 989. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Cai, X. Huang, C. Liu, F. Rosamond, and Y. Song Parameterized Complexity and Biopolymer Sequence Comparison The Computer Journal, May 1, 2008; 51(3): 270 - 291. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. M. Overton, G. Padovani, M. A. Girolami, and G. J. Barton ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction Bioinformatics, April 1, 2008; 24(7): 901 - 907. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Singh A review of algorithmic techniques for disulfide-bond determination Brief Funct Genomic Proteomic, March 27, 2008; (2008) eln008v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Gong and G. D. Rose Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model PNAS, March 4, 2008; 105(9): 3321 - 3326. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Ikura, K. Kinoshita, and N. Ito A cavity with an appropriate size is the basis of the PPIase activity Protein Eng. Des. Sel., February 1, 2008; 21(2): 83 - 89. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. S. Wishart, D. Arndt, M. Berjanskii, A. C. Guo, Y. Shi, S. Shrivastava, J. Zhou, Y. Zhou, and G. Lin PPT-DB: the protein property prediction and testing database Nucleic Acids Res., January 11, 2008; 36(suppl_1): D222 - D229. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. H. Dessailly, M. F. Lensink, C. A. Orengo, and S. J. Wodak LigASite a database of biologically relevant binding sites in proteins with known apo-structures Nucleic Acids Res., January 11, 2008; 36(suppl_1): D667 - D673. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. DiMaio, D. A. Kondrashov, E. Bitto, A. Soni, C. A. Bingman, G. N. Phillips Jr, and J. W. Shavlik Creating protein models from electron-density maps using particle-filtering methods Bioinformatics, November 1, 2007; 23(21): 2851 - 2858. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Gong, Y. Shen, and G. D. Rose Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly Protein Sci., August 1, 2007; 16(8): 1515 - 1521. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. O. Street, N. C. Fitzkee, L. L. Perskie, and G. D. Rose Physical-chemical determinants of turn conformations in globular proteins Protein Sci., August 1, 2007; 16(8): 1720 - 1727. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Terribilini, J. D. Sander, J.-H. Lee, P. Zaback, R. L. Jernigan, V. Honavar, and D. Dobbs RNABindR: a server for analyzing and predicting RNA-binding sites in proteins Nucleic Acids Res., July 13, 2007; 35(suppl_2): W578 - W584. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. E. Felder, J. Prilusky, I. Silman, and J. L. Sussman A server and database for dipole moments of proteins Nucleic Acids Res., July 13, 2007; 35(suppl_2): W512 - W521. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Ishida and K. Kinoshita PrDOS: prediction of disordered protein regions from amino acid sequence Nucleic Acids Res., July 13, 2007; 35(suppl_2): W460 - W464. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Wu, M. Lu, M. Chen, J. Li, and J. Ma OPUS-Ca: A knowledge-based potential function requiring only C{alpha} positions Protein Sci., July 1, 2007; 16(7): 1449 - 1463. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Hartmann, I. Antes, and T. Lengauer IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models Protein Sci., July 1, 2007; 16(7): 1294 - 1307. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Zhou, B. Xue, and Y. Zhou DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile Protein Sci., May 1, 2007; 16(5): 947 - 955. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Sacan, O. Ozturk, H. Ferhatosmanoglu, and Y. Wang LFM-Pro: a tool for detecting significant local structural sites in proteins Bioinformatics, March 15, 2007; 23(6): 709 - 716. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Z. Spassov, L. Yan, and P. K. Flook The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: A side-chain prediction algorithm based on side-chain backbone interactions Protein Sci., March 1, 2007; 16(3): 494 - 506. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Wollacott, A. Zanghellini, P. Murphy, and D. Baker Prediction of structures of multidomain proteins from structures of the individual domains Protein Sci., February 1, 2007; 16(2): 165 - 175. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-B. Shen and K.-C. Chou Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins Protein Eng. Des. Sel., January 23, 2007; (2007) gzl053v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Xu, A. Canutescu, Z. Obradovic, and R. L. Dunbrack Jr ProtBuD: a database of biological unit structures of protein families and superfamilies Bioinformatics, December 1, 2006; 22(23): 2876 - 2882. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M.-y. Shen and A. Sali Statistical potential for assessment and prediction of protein structures. Protein Sci., November 1, 2006; 15(11): 2507 - 2524. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Douguet, H.-C. Chen, A. Tovchigrechko, and I. A. Vakser DOCKGROUND resource for studying protein-protein interfaces Bioinformatics, November 1, 2006; 22(21): 2612 - 2618. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. O. Yesylevskyy, V. N. Kharkyanen, and A. P. Demchenko The Change of Protein Intradomain Mobility on Ligand Binding: Is It a Commonly Observed Phenomenon? Biophys. J., October 15, 2006; 91(8): 3002 - 3013. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Sawada and S. Honda Structural Diversity of Protein Segments Follows a Power-Law Distribution Biophys. J., August 15, 2006; 91(4): 1213 - 1223. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Terribilini, J.-H. Lee, C. Yan, R. L. Jernigan, V. Honavar, and D. Dobbs Prediction of RNA binding sites in proteins from amino acid sequence RNA, August 1, 2006; 12(8): 1450 - 1462. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. O. Yesylevskyy, V. N. Kharkyanen, and A. P. Demchenko Dynamic Protein Domains: Identification, Interdependence, and Stability Biophys. J., July 15, 2006; 91(2): 670 - 685. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. S. Cerutti, T. Jain, and J. A. McCammon CIRSE: A solvation energy estimator compatible with flexible protein docking and design applications. Protein Sci., July 1, 2006; 15(7): 1579 - 1596. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-C. Gelly, C. Etchebest, S. Hazout, and A.G. de Brevern Protein Peeling 2: a web server to convert protein structures into series of protein units. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W75 - W78. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Parthiban, M. M. Gromiha, and D. Schomburg CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W239 - W242. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Bandyopadhyay, J. Huan, J. Liu, J. Prins, J. Snoeyink, W. Wang, and A. Tropsha Structure-based function inference using protein family-specific fingerprints. Protein Sci., June 1, 2006; 15(6): 1537 - 1543. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Dehouck, D. Gilis, and M. Rooman A New Generation of Statistical Potentials for Proteins Biophys. J., June 1, 2006; 90(11): 4010 - 4017. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Hoskins, S. Lovell, and T. L. Blundell An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements. Protein Sci., May 1, 2006; 15(5): 1017 - 1029. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. S. Chapman A structurally-defined gap function for pairwise sequence alignment of proteins in the twilight zone FASEB J, March 1, 2006; 20(5): A928 - A928.
|
|
|
|
|
|
J.-C. Gelly, A. G. de Brevern, and S. Hazout 'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments Bioinformatics, January 15, 2006; 22(2): 129 - 133. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Gong, P. J. Fleming, and G. D. Rose From The Cover: Building native protein conformation from highly approximate backbone torsion angles PNAS, November 8, 2005; 102(45): 16227 - 16232. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Panasik Jr., P. J. Fleming, and G. D. Rose Hydrogen-bonded turns in proteins: The case for a recount Protein Sci., November 1, 2005; 14(11): 2910 - 2914. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. K. Jha, A. Colubri, K. F. Freed, and T. R. Sosnick Statistical coil model of the unfolded state: Resolving the reconciliation problem PNAS, September 13, 2005; 102(37): 13099 - 13104. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Alland, F. Moreews, D. Boens, M. Carpentier, S. Chiusa, M. Lonquety, N. Renault, Y. Wong, H. Cantalloube, J. Chomilier, et al. RPBS: a web resource for structural bioinformatics Nucleic Acids Res., July 1, 2005; 33(suppl_2): W44 - W49. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Laskowski, J. D. Watson, and J. M. Thornton ProFunc: a server for predicting protein function from 3D structure Nucleic Acids Res., July 1, 2005; 33(suppl_2): W89 - W93. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Wang and R. L. Dunbrack Jr PISCES: recent improvements to a PDB sequence culling server Nucleic Acids Res., July 1, 2005; 33(suppl_2): W94 - W98. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Wang, O. Schueler-Furman, and D. Baker Improved side-chain modeling for protein-protein docking Protein Sci., May 1, 2005; 14(5): 1328 - 1339. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Gront and A. Kolinski A new approach to prediction of short-range conformational propensities in proteins Bioinformatics, April 1, 2005; 21(7): 981 - 987. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. G. P. Swarts, J. B. Koenderink, P. H. G. M. Willems, E. Krieger, and J. J. H. H. M. De Pont Asn792 Participates in the Hydrogen Bond Network Around the K+-binding Pocket of Gastric H,K-ATPase J. Biol. Chem., March 25, 2005; 280(12): 11488 - 11494. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. G. Krishna and S. W. Englander The N-terminal to C-terminal motif in protein folding and function PNAS, January 25, 2005; 102(4): 1053 - 1058. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. J. Fleming, N. C. Fitzkee, M. Mezei, R. Srinivasan, and G. D. Rose A novel method reveals that solvent water favors polyproline II over {beta}-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA) Protein Sci., January 1, 2005; 14(1): 111 - 118. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Jaramillo and S. J. Wodak Computational Protein Design Is a Challenge for Implicit Solvation Models Biophys. J., January 1, 2005; 88(1): 156 - 171. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Bhattacharyya, D. Pal, and P. Chakrabarti Disulfide bonds, their stereospecific environment and conservation in protein structures Protein Eng. Des. Sel., November 1, 2004; 17(11): 795 - 808. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Dehouck, D. Gilis, and M. Rooman Database-Derived Potentials Dependent on Protein Size for In Silico Folding and Design Biophys. J., July 1, 2004; 87(1): 171 - 181. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Gautier, A.-C. Camproux, and P. Tuffery SCit: web tools for protein side chain conformation analysis Nucleic Acids Res., July 1, 2004; 32(suppl_2): W508 - W511. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Guyon, A.-C. Camproux, J. Hochez, and P. Tuffery SA-Search: a web tool for protein structure mining based on a Structural Alphabet Nucleic Acids Res., July 1, 2004; 32(suppl_2): W545 - W548. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. A. Ivanisenko, S. S. Pintus, D. A. Grigorovich, and N. A. Kolchanov PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins Nucleic Acids Res., July 1, 2004; 32(suppl_2): W549 - W554. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. B. Holmes and J. Tsai Some fundamental aspects of building protein structures from fragment libraries Protein Sci., June 1, 2004; 13(6): 1636 - 1650. [Abstract] [Full Text] [PDF]
|
|