SCRATCH: a Protein Structure and Structural Feature Prediction Server

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2005 Jun 28

PMID 15980571

Citations 438

Authors

J Cheng

A Z Randall

M J Sweredoski

P Baldi

Affiliations

Soon will be listed here.

Abstract

SCRATCH is a server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. The user simply provides an amino acid sequence and selects the desired predictions, then submits to the server. Results are emailed to the user. The server is available at http://www.igb.uci.edu/servers/psss.html.

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References

Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H . The Protein Data Bank. Nucleic Acids Res. 1999; 28(1):235-42. PMC: 102472. DOI: 10.1093/nar/28.1.235. View

Simons K, Ruczinski I, Kooperberg C, Fox B, Bystroff C, Baker D . Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins. 1999; 34(1):82-95. DOI: 10.1002/(sici)1097-0134(19990101)34:1<82::aid-prot7>3.0.co;2-a. View

Eyrich V, Przybylski D, Madhusudhan M, Fiser A, Pazos F, Valencia A . EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics. 2001; 17(12):1242-3. DOI: 10.1093/bioinformatics/17.12.1242. View

Przybylski D, Rost B . Alignments grow, secondary structure prediction improves. Proteins. 2002; 46(2):197-205. DOI: 10.1002/prot.10029. View

Pollastri G, Baldi P, Fariselli P, Casadio R . Prediction of coordination number and relative solvent accessibility in proteins. Proteins. 2002; 47(2):142-53. DOI: 10.1002/prot.10069. View

Pollastri G, Przybylski D, Rost B, Baldi P . Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins. 2002; 47(2):228-35. DOI: 10.1002/prot.10082. View

Pollastri G, Baldi P . Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics. 2002; 18 Suppl 1:S62-70. DOI: 10.1093/bioinformatics/18.suppl_1.s62. View

Canutescu A, Shelenkov A, Dunbrack Jr R . A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 2003; 12(9):2001-14. PMC: 2323997. DOI: 10.1110/ps.03154503. View

Moult J, Fidelis K, Zemla A, Hubbard T . Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins. 2003; 53 Suppl 6:334-9. DOI: 10.1002/prot.10556. View

10.

Kabsch W, Sander C . Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983; 22(12):2577-637. DOI: 10.1002/bip.360221211. View

11.

Holm L, Sander C . Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. J Mol Biol. 1991; 218(1):183-94. DOI: 10.1016/0022-2836(91)90883-8. View

12.

Simons K, Kooperberg C, Huang E, Baker D . Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol. 1997; 268(1):209-25. DOI: 10.1006/jmbi.1997.0959. View

13.

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

14.

Vendruscolo M, Kussell E, Domany E . Recovery of protein structure from contact maps. Fold Des. 1997; 2(5):295-306. DOI: 10.1016/S1359-0278(97)00041-2. View

15.

Pearl F, Lee D, Bray J, Sillitoe I, Todd A, Harrison A . Assigning genomic sequences to CATH. Nucleic Acids Res. 1999; 28(1):277-82. PMC: 102424. DOI: 10.1093/nar/28.1.277. View