Use of secondary structural information and Cα-Cα distance restraints to model protein structures with MODELLER

Journal of Biosciences

Volumn 32, Issue 1, 2007, Pages 929-936

  Reddy, Boojala V B ^a   Kaznessis, Yiannis N ^b  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b University of Minnesota   (United States)

Author keywords

Model evolution; Protein modelling; Residue contact prediction; Secondary structure prediction

Indexed keywords

AMINO ACID; OPTIMIZATION; PROTEIN;

ALPHA HELIX; AMINO ACID SEQUENCE; CONFERENCE PAPER; MOLECULAR MODEL; PREDICTION; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE;

EID: 34548762596     PISSN: 02505991     EISSN: 02505991     Source Type: Journal    
DOI: 10.1007/s12038-007-0093-1     Document Type: Conference Paper

References (27)

1. Brocklehurst S M and Perham R N 1993 Prediction of the three-dimensional structures of the biotinylated domain from yeast pyruvate carboxylase and of the lipoylated H-protein from the pea leaf glycine cleavage system: a new automated method for the prediction of protein tertiary structure; Protein Sci. 2 626-639
2. Chandonia J M and Karplus M 1996 The importance of larger data sets for protein secondary structure prediction with neural networks; Protein Sci. 5 768-774
3. Chandonia J M and Karplus M 1999 New methods for accurate prediction of protein secondary structure; Proteins 35 293-306
4. Crivelli, S, Kreylos O, Hamann B, Max N and Bethel W 2004 ProteinShop: a tool for interactive protein manipulation and steering; J. Comput. Aided Mol. Des. 18 271-285
5. Fariselli P and Casadio R 1999 A neural network based predictor of residue contacts in proteins; Protein Eng. 12 15-21
6. Fariselli P, Olmea O, Valencia A and Casadio R 2001a Prediction of contact maps with neural networks and correlated mutations; Protein Eng. 14 835-843
7. Fariselli P, Olmea O, Valencia A and Casadio R 2001b Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations; Proteins Suppl. 5 157-162
8. Fiser A and Sali A 2003 Modeller: generation and refinement of homology-based protein structure models; Methods Enzymol. 374 461-491
9. Hamilton N, Burrage K, Ragan M A and Huber T 2004 Protein contact prediction using patterns of correlation; Proteins 56 679-684
10. Hung L H and Samudrala R 2003 Accurate and automated classification of protein secondary structure with PsiCSI; Protein Sci. 12 288-295
11. Jiang F 2003 Prediction of protein secondary structure with a reliability score estimated by local sequence clustering; Protein Eng. 16 651-657
12. Kabsch W and Sander C 1983 Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features; Biopolymers 22 2577-2637
13. Kolinski A, Betancourt M R, Kihara D, Rotkiewicz P and Skolnick J 2001 Generalized comparative modelling (GENECOMP): a combination of sequence comparison, threading, and lattice modelling for protein structure prediction and refinement; Proteins 44 133-149
14. Lee B and Richards F M 1971 The interpretation of protein structures: estimation of static accessibility; J. Mol. Biol. 55 379-400
15. Lin K, Simossis V A, Taylor W R and Heringa J 2004 A simple and fast secondary structure prediction method using hidden neural networks; Bioinformatics 21 152-159
16. MacCallum R M 2004 Striped sheets and protein contact prediction; Bioinformatics (Suppl.) 20 I224-I231
17. Moglich A, Weinfurtner D, Gronwald W, Maurer T and Kalbitzer H R 2005. PERMOL: restraint-based protein homology modelling using DYANA or CNS; Bioinformatics 21 2110-2111
18. Moult J, Fidelis K, Zemla A and Hubbard T 2003 Critical assessment of methods of protein structure prediction (CASP)-round V; Proteins (Suppl. 6) 53 334-339
19. Petersen T N, Lundegaard C, Nielsen M, Bohr H, Bohr J, Brunak S, Gippert G P et al 2000 Prediction of protein secondary structure at 80% accuracy; Proteins 41 17-20
20. Reddy B, and Kaznessis Y 2005 A Quantitative analysis of amino acid position conservation in interface regions of protein-protein hetrocomplexes; J. Bioinfo. Comput. Bio. 3 1137-1150
21. Sali A and Blundell T L 1993 Comparative protein modelling by satisfaction of spatial restraints; J. Mol. Biol. 234 779-815
22. Siew N, Elofsson A, Rychlewski L and Fischer D 2000 MaxSub: an automated measure for the assessment of protein structure prediction quality; Bioinformatics 16 776-785
23. Wood M J and Hirst J D 2004 Predicting protein secondary structure by cascade-correlation neural networks; Bioinformatics 20 419-420
24. Wu K P, Lin H N, Chang J M, Sung T Y and Hsu W L 2004 HYPROSP: a hybrid protein secondary structure prediction algorithm - a knowledge-based approach; Nucleic Acids Res. 32 5059-5065
25. Zemla A, Venclovas C, Moult J and K Fidelis K 1999 Processing and analysis of CASP3 protein structure predictions; Proteins (Suppl.) 3 22-29
26. Zhang C, Hou J and Kim S H 2002 Fold prediction of helical proteins using torsion angle dynamics and predicted restraints; Proc. Natl. Acad. Sci. USA 99 3581-3585
27. Zhang Y and Skolnick J 2004 Scoring function for automated assessment of protein structure template quality; Proteins 57 702-710