PISCES

PISCES: a protein sequence culling server. 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


References in zbMATH (referenced in 31 articles )

Showing results 1 to 20 of 31.
Sorted by year (citations)

1 2 next

  1. Mei, Juan; Fu, Yi; Zhao, Ji: Analysis and prediction of ion channel inhibitors by using feature selection and Chou’s general pseudo amino acid composition (2018)
  2. Wong, Samuel W. K.; Liu, Jun S.; Kou, S. C.: Exploring the conformational space for protein folding with sequential Monte Carlo (2018)
  3. Zhang, Shengli; Liang, Yunyun: Predicting apoptosis protein subcellular localization by integrating auto-cross correlation and PSSM into Chou’s PseAAC (2018)
  4. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  5. Simon Mitternacht: FreeSASA: An open source C library for solvent accessible surface area calculations (2016) arXiv
  6. Fernandez-Lozano, Carlos; Cuiñas, Rubén F.; Seoane, José A.; Fernández-Blanco, Enrique; Dorado, Julian; Munteanu, Cristian R.: Classification of signaling proteins based on molecular star graph descriptors using machine learning models (2015)
  7. Fernandez-Lozano, Carlos; Gestal, Marcos; González-Díaz, Humberto; Dorado, Julián; Pazos, Alejandro; Munteanu, Cristian R.: Markov mean properties for cell death-related protein classification (2014)
  8. Mahalingam, Rajasekaran; Peng, Hung-Pin; Yang, An-Suei: Prediction of FMN-binding residues with three-dimensional probability distributions of interacting atoms on protein surfaces (2014)
  9. Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan: GOASVM: a subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou’s pseudo-amino acid composition (2013)
  10. Li, Tao; Li, Qian-Zhong: Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure (2012)
  11. de Sousa, Miguel M.; Munteanu, Cristian R.; Pazos, Alejandro; Fonseca, Nuno A.; Camacho, Rui; Magalhães, A. L.: Amino acid pair- and triplet-wise groupings in the interior of (\alpha)-helical segments in proteins (2011)
  12. Lee, Jinwoo: Using an abstraction of amino acid types to improve the quality of statistical potentials for protein structure prediction (2011)
  13. Srivastava, Sheenal; Patton, Yumi; Fisher, David W.; Wood, Graham R.: Cotranslational protein folding and terminus hydrophobicity (2011) ioport
  14. Zarić, Božidarka L.; Jovanović, Vesna B.; Stojanović, Srđan Đ.: Non-covalent interactions across subunit interfaces in Sm proteins (2011)
  15. Zhang, Lei; Zhang, Ning; Ruan, Ji-Shou; Zhang, Tao: Studies on the rules of (\beta)-strand alignment in a protein (\beta)-sheet structure (2011)
  16. Bakheet, Tala; Doig, Andrew J.: Properties and identification of antibiotic drug targets (2010) ioport
  17. Zhang, Ning; Duan, Guangyou; Gao, Shan; Ruan, Jishou; Zhang, Tao: Prediction of the parallel/antiparallel orientation of beta-strands using amino acid pairing preferences and support vector machines (2010)
  18. Chen, Bernard; Johnson, Matthew: Protein local 3D structure prediction by super granule support vector machines (Super GSVM) (2009) ioport
  19. Ramana, Jayashree; Gupta, Dinesh: Lipocalinpred: a SVM-based method for prediction of lipocalins (2009) ioport
  20. Strömbergsson, Helena; Kleywegt, Gerard J.: A chemogenomics view on protein-ligand spaces (2009) ioport

1 2 next