Surface-histogram: A new shape descriptor for protein-protein docking

Proteins: Structure, Function and Bioinformatics

Volumn 80, Issue 1, 2012, Pages 221-238

  Gu, Shengyin ^a   Koehl, Patrice ^a,b   Hass, Joel ^b   Amenta, Nina ^a  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Protein surface; Protein protein docking; Shape descriptor; Surface histogram

Indexed keywords

DOCKING PROTEIN;

ALGORITHM; ARTICLE; CONTROLLED STUDY; HISTOGRAM; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; QUALITY CONTROL;

ALGORITHMS; COMPUTER SIMULATION; DATA COMPRESSION; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, QUATERNARY; SOFTWARE; SURFACE PROPERTIES;

EID: 83555176324     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23192     Document Type: Article

References (35)

1. Baker M, Zhang J, Ludtke S, Chiu W. Cryo-EM of macromolecular assemblies at near-atomic resolution. Nat Protoc 2010; 5: 1697-1708.
2. Ritchie DW. Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 2008; 9: 1-15.
3. Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins: Struct Funct Genet 2002; 47: 409-443.
4. Smith GR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002; 12: 28-35.
5. Méndez R, Leplae R, Maria LD, Wodak SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins: Struct Funct Genet 2003; 52: 51-67.
6. Vajda S, Kozakov D. Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol 2009; 19: 164-170.
7. Janin J. Protein-protein docking tested in blind predictions: the CAPRI experiment. Mol Biosyst 2010; 6: 2351-2362.
8. Fernández-Recio J, Totrov M, Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins: Struct Funct Genet 2003; 52: 113-117.
9. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003; 331: 281-299.
10. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992; 89: 2195-2199.
11. Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein docking algorithm. Proteins: Struct Funct Bioinform 2003; 52: 80-87.
12. Kozakov D, Brenke R, Comeau SR, Vajda S. Piper: an FFT-based protein docking program with pairwise potentials. Proteins: Struct Funct Bioinform 2006; 65: 392-406.
13. Kowalsman N, Eisenstein M. Inherent limitations in protein-protein docking procedures. Bioinformatics 2007; 23: 421-426.
14. Gabb HA, Jackson RM, Sternberg MJE. Modelling protein docking using shape complementarity, electrostatics, and biochemical information. J Mol Biol 1997; 272: 106-120.
15. Vasker IA. Protein docking for low-resolution strutures. Protein Eng 1995; 8: 371-377.
16. Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, Tsigelny I, Eyck LFT. Protein docking using continuum electrostatics and geometric fit. Protein Eng 2001; 14: 105-113.
17. Duhovny D, Nussinov R, Wolfson HJ. Efficient unbound docking of rigid molecules. In: WABI ′02: Proceedings of the Second International Workshop on Algorithms in Bioinformatics. Springer-Verlag: London, UK 2002. pp. 185-200.
18. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. Geometry-based flexible and symmetric protein docking. Proteins: Struct Funct Bioinform 2005; 60: 224-231.
19. Ritchie D, Kemp G. Protein docking using spherical polar fourier correlations. Proteins: Struct Funct Genet 2000; 39: 178-194.
20. Shentu Z, Hasan M, Bystroff C, Zaki M. Context shapes: efficient complementary shape matching for protein-protein docking. Proteins: Struct Funct Bioinform 2008; 70: 1056-1073.
21. Venkatraman V, Yang Y, Sael L, Kihara D. Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinform 2009; 10: 407.
22. Bock ME, Cortelazzo GM, Ferrari C, Guerra C. Identifying similar surface patches on proteins using a spin-image surface representation. In: Apostolico A, Crochemore M, Park K, editors. Combinatorial pattern matching. Lecture Notes in Computer Science Vol. 3537 Berlin/Heidelberg; Springer: 2005. pp. 417-428.
23. Canterakis N. 3D Zernike moments and Zernike affine invariants for 3D image analysis and recognition. In: Proceedings of the 11th Scandinavian conference on image analysis, Kanger-lussuaq, Greenland (Denmark). 1999. pp. 85-93.
24. Beygelzimer A, Kakade S, Langford J. Cover trees for nearest neighbor. In: Proceedings of the 23rd international conference on machine learning, ICML ′06. New York, NY, USA; ACM: 2006. pp. 97-104.
25. Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins: Struct Funct Bioinform 2008; 73: 705-709.
26. Cipriano G, Phillips GN, Jr, Gleicher M. Multi-scale surface descriptors. IEEE Trans Vis Comput Graph 2009; 15: 1201-1208.
27. Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z. Protein-protein docking benchmark 2.0: an update. Proteins Struct Functt Bioinform 2005; 60: 214-216.
28. dms program. Available at
29. Connolly M. Analytical molecular surface calculation. J Appl Crystalogr 1983; 16: 548-558.
30. Gribskov M, Robinson N. Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput Chem 1996; 20: 25-33.
31. Pierce B, Hourai Y, Weng Z. ZDOCK 2.3.1 and ZDOCK 3.0.1: using a new 3D convolution library to enhance docking efficiency, submitted.
32. Gabdoulline R, Wade R, Walther D. MolSurfer: a macromolecular interface navigator. Nucleic Acids Res 2003; 31: 3349-3351.
33. Bock ME, Garutti C, Guerra C. Discovery of similar regions on protein surfaces. J Comput Biol 2007; 14: 285-299.
34. Francis-Lyon P, Gu S, Hass J, Amenta N, Koehl P. Sampling the conformation of protein surface residues for flexible protein docking. BMC Bioinform 2010; 11: 575-588.
35. CUDA. Supercomputing for the masses: Part 1. Available at