SPOT-Seq-RNA: Predicting protein–RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction

Methods in Molecular Biology

Volumn 1137, Issue , 2014, Pages 119-130

  Yang, Yuedong ^a   Zhao, Huiying ^a   Wang, Jihua ^a   Zhou, Yaoqi ^a  

^a NONE

Author keywords

Binding affinity; Fold recognition; Knowledge based energy function; Prediction; Protein RNA complex structure; Protein RNA interactions; RNA binding proteins; Solvent accessible surface area; SPOT Seq RNA; Template based structure prediction; Torsion angle prediction

Indexed keywords

AMINO ACID; MULTIPROTEIN COMPLEX; PROTEIN RNA COMPLEX; RIBONUCLEASE H; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; RNA;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; COMPUTER PROGRAM; HUMAN; HUMAN GENOME; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; RNA STRUCTURE; SEQUENCE HOMOLOGY; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; GENETIC DATABASE; PROTEIN BINDING; WEB BROWSER;

BINDING SITES; DATABASES, GENETIC; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN BINDING; RNA; RNA-BINDING PROTEINS; SOFTWARE; WEB BROWSER;

EID: 84907873774     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0366-5_9     Document Type: Article

References (28)

1. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 112: 535-542.
2. Tsvetanova NG, Klass DM, Salzman J, Brown PO (2010) Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PLoS One 5: e12671.
3. Scherrer T, Mittal N, Janga SC, Gerber AP (2010) A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes. PLoS One 5: e15499.
4. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM et al (2012) Insights into RNA biology from an Atlas of mammalian mRNA-binding proteins. Cell 149: 1393-1406.
5. Puton T, Kozlowski L, Tuszynska I, Rother K, Bujnicki JM (2012) Computational methods for prediction of protein-RNA interactions. J Struct Biol 179(3): 261-8.
6. Walia RR, Caragea C, Lewis BA, Towfic FG, Terribilini M, El-Manzalawy Y, Dobbs D, Honavar V (2012) Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. BMC Bioinformatics 13: 89.
7. Perez-Cano L, Solernou A, Pons C, Fernandez-Recio J (2010) Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials. Pac Symp Biocomput 15: 269-280.
8. Zheng S, Robertson TA, Varani G (2007) A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins. FEBS J 274: 6378-6391.
9. Tuszynska I, Bujnicki JM (2011) DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. BMC Bioinformatics 12: 348.
10. Setny P, Zacharias M (2011) A coarse-grained force field for Protein-RNA docking. Nucleic Acids Res 39: 9118-9129.
11. Zhao H, Yang Y, Zhou Y (2011) Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction. RNA Biol 8: 988-996.
12. Yang Y, Faraggi E, Zhao H, Zhou Y (2011) Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of the query and corresponding native properties of templates. Bioinformatics 27: 2076-2082.
13. Zhou HY, Zhou Y (2005) SPARKS 2 and SP3 servers in CASP 6. Proteins 61: 152-156.
14. Liu S, Zhang C, Liang SD, Zhou Y (2007) Fold recognition by concurrent use of solvent accessibility and residue depth. Proteins 68: 636-645.
15. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
16. Faraggi E, Yang YD, Zhang SS, Zhou Y (2009) Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction. Structure 17: 1515-1527.
17. Faraggi E, Zhang T, Yang Y, Kurgan L, Zhou Y (2011) SPINE X: improving protein secondary structure prediction by multi-step learning coupled with prediction of solvent accessible surface area and backbone torsion angles. J Comput Chem 33: 259-263.
18. Faraggi E, Xue B, Zhou Y (2009) Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network. Proteins 74: 847-856.
19. Zhao HY, Yang YD, Zhou YQ (2011) Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Res 39: 3017-3025.
20. Zhou HY, Zhou Y (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 11: 2714-2726.
21. Zhou Y, Zhou HY, Zhang C, Liu S (2006) What is a desirable statistical energy function for proteins and how can it be obtained? Cell Biochem Biophys 46: 165-174.
22. Zhou YQ, Duan Y, Yang YD, Faraggi E, Lei HX (2011) Trends in template/fragment-free protein structure prediction. Theor Chem Acc 128: 3-16.
23. Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33: W244-W248.
24. Zhao H, Yang Y, Zhou Y (2013) Prediction of RNA binding proteins comes of age from low resolution to high resolution. Mol Biosyst 9(10): 2417-25.
25. Zhao H, Yang Y, Janga SC, Kao C, Zhou Y (2013) Prediction and validation of the unexplored RNA-binding protein atlas of the human genome. Proteins, in press (doi: 10. 1002/prot. 24441).
26. Nowotny M, Gaidamakov SA, Crouch RJ, Yang W (2005) Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell 121: 1005-1016.
27. Dor O, Zhou Y (2007) Achieving 80 % ten-fold cross-validated accuracy for secondary structure prediction by large-scale training. Proteins 66: 838-845.
28. Yang Y, Zhan J, Zhao H, Zhou Y (2012) A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction. Proteins 80: 2080-2088.