Achievements and challenges in structural bioinformatics and computational biophysics

Bioinformatics

Volumn 31, Issue 1, 2015, Pages 146-150

  Samish, Ilan ^a,b   Bourne, Philip E ^c   Najmanovich, Rafael J ^d  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b ORT BRAUDE COLLEGE   (Israel)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d UNIVERSITY OF SHERBROOKE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACHIEVEMENT; BIOLOGY; BIOPHYSICS; HUMAN; MEDICAL RESEARCH; TRENDS;

ACHIEVEMENT; BIOMEDICAL RESEARCH; BIOPHYSICS; COMPUTATIONAL BIOLOGY; HUMANS;

EID: 84922390208     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu769     Document Type: Article

References (77)

1. Adams,J. (2003) The proteasome: structure, function, and role in the cell. Cancer Treat Rev., 29 (Suppl. 1), 3-9.
2. Adcock,S.A. and McCammon,J.A. (2006) Molecular dynamics: survey of methods for simulating the activity of proteins. Chem. Rev., 106, 1589-1615.
3. Anderson,D.P. (2004) BOINC: a system for public-resource computing and storage. In: Fifth IEEE/ACM International Workshop on Grid Computing. IEEE, pp. 4-10, Nov. 8, 2004. IEEE. doi: http://10.1109/GRID.2004.14.
4. Andreeva,A. et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res., 36, D419-D25.
5. Baase,W.A. et al. (2010) Lessons from the lysozyme of phage T4. Protein Sci., 19, 631-641.
6. Bahar,I. and Rader,A.J. (2005) Coarse-grained normal mode analysis in structural biology. Curr. Opin. Struct. Biol., 15, 586-592.
7. Baker,D. and Sali,A. (2001) Protein structure prediction and structural genomics. Science, 294, 93-96.
8. Beauchamp,K.A. et al. (2011) MSMBuilder2: modeling conformational dynamics at the picosecond to millisecond scale. J. Chem. Theory Comput., 7, 3412-3419.
9. Berman,H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
10. Bourne,P.E. (2003) CASP and CAFASP experiments and their findings. Methods Biochem. Anal., 44, 501-507.
11. Brooijmans,N. and Kuntz,I.D. (2003) Molecular recognition and docking algorithms. Annu. Rev. Biophys. Biomol. Struct., 32, 335-373.
12. Chang,R.L. et al. (2010) Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput. Biol., 6, e1000938.
13. Chothia,C. and Janin,J. (1975) Principles of protein-protein recognition. Nature, 256, 705-708.
14. Cooper,S. et al. (2010) Predicting protein structures with a multiplayer online game. Nature, 466, 756-760.
15. Dill,K.A. and Chan,H.S. (1997) From Levinthal to pathways to funnels. Nat. Struct. Biol., 4, 10-19.
16. Ellis,R. (2001) Macromolecular crowding: an important but neglected aspect of the intracellular environment. Curr. Opin. Struct. Biol., 11, 114-119.
17. Eswar,N. et al. (2007) Protein structure modeling withMODELLER. MethodsMol. Biol., 426, 145-159.
18. Finn,R.D. et al. (2014) Pfam: the protein families database. Nucleic Acids Res., 42, D222-D230.
19. Frappier,V. and Najmanovich,R.J. (2014) A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations. PLoS Comput. Biol., 10, e1003569.
20. Friedrichs,M.S. et al. (2009) Accelerating molecular dynamic simulation on graphics processing units. J. Comput. Chem., 30, 864-872.
21. Gerlt,J.A. and Babbitt,P.C. (2009) Enzyme (re)design: lessons from natural evolution and computation. Curr. Opin. Chem. Biol., 13, 10-18.
22. Ginalski,K. et al. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics, 19, 1015-1018.
23. Gu,J. and Bourne,P.E. (2011) Structural bioinformatics. Wiley-Blackwell.
24. Hallock,M.J. et al. (2014) Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations. Parallel Comput., 40, 86-99.
25. Halperin,I. et al. (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins, 47, 409-443.
26. Hynninen,A.-P. and Crowley,M.F. (2014) New faster CHARMM molecular dynamics engine. J. Comput. Chem., 35, 406-413.
27. Janin,J. et al. (2003) CAPRI: a critical assessment of predicted interactions. Proteins, 52, 2-9.
28. Jones,S. and Thornton,J.M. (1996) Principles of protein-protein interactions. Proc. Natl Acad. Sci. USA, 93, 13-20.
29. Karplus,M. (1997) The Levinthal paradox: yesterday and today. Fold Des., 2, S69-S75.
30. Khoury,G.A. et al. (2014) WeFold: a coopetition for protein structure prediction. Proteins, 82, 1850-1868.
31. Kinnings,S.L. et al. (2009) Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput. Biol., 5, e1000423.
32. Kiss,G. et al. (2013) Computational enzyme design. Angew. Chem. Int. Ed. Engl., 52, 5700-5725.
33. Kitchen,D.B. et al. (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug. Discov., 3, 935-949.
34. Kufareva,I. et al. (2014) Advances in GPCR modeling evaluated by the GPCR dock 2013 assessment: meeting new challenges. Structure, 22, 1120-1139.
35. Kurbatova,N. et al. (2013) IsoCleft finder-A web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities. F1000Res, 2, 117.
36. Laing,C. and Schlick,T. (2010) Computational approaches to 3D modeling of RNA. J. Phys. Condens. Matter, 22, 283101.
37. Levitt,M. (2001) The birth of computational structural biology. Nat. Struct. Mol. Biol., 8, 392-393.
38. Levy,E.D. et al. (2008) Assembly reflects evolution of protein complexes. Nature, 453, 1262-1265.
39. Marchisio,M.A. and Stelling,J. (2009) Computational design tools for synthetic biology. Curr. Opin. Biotechnol., 20, 479-485.
40. Marks,D.S. et al. (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS One, 6, e28766.
41. Masum,H. et al. (2013) Ten simple rules for cultivating open science and collaborative R&D. PLoS Comput. Biol., 9, e1003244.
42. McGuffee,S.R. and Elcock,A.H. (2010) Diffusion, crowding &protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput. Biol., 6, e1000694.
43. Minton,A. (1993) Macromolecular crowding and molecular recognition. J. Mol. Recognit., 6, 211-214.
44. Moult,J. et al. (2014) Critical assessment of methods of protein structure prediction (CASP)-round x. Proteins, 82 (Suppl. 2), 1-6.
45. Najmanovich,R. et al. (2008) Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites. Bioinformatics, 24, i105-i111.
46. Najmanovich,R.J. et al. (2005) Prediction of protein function from structure: insights from methods for the detection of local structural similarities. BioTechniques, 38, 847, 849, 851.
47. Nugent,T. and Jones,D.T. (2012) Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proc. Natl Acad. Sci. USA, 109, E1540-E1547.
48. Ollikainen,N. et al. (2013) Flexible backbone sampling methods to model and design protein alternative conformations. Methods Enzymol., 523, 61-85.
49. Parisien,M. and Major,F. (2012) Determining RNA three-dimensional structures using low-resolution data. J. Struct. Biol., 179, 252-260.
50. Patel,M.S. et al. (2014) The pyruvate dehydrogenase complexes: structure-based function and regulation. J. Biol. Chem., 289, 16615-16623.
51. Peterson,J.R. et al. (2014) Towards a computational model of a methane producing archaeum. Archaea, 2014, 898453.
52. Potapov,V. et al. (2008) Computational redesign of a protein-protein interface for high affinity and binding specificity using modular architecture and naturally occurring template fragments. J. Mol. Biol., 384, 109-119.
53. Potterton,L. et al. (2004) Developments in the CCP4 molecular-graphics project. Acta Crystallogr. D, 60, 2288-2294.
54. Pronk,S. et al. (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29, 845-854.
55. Radivojac,P. et al. (2013) A large-scale evaluation of computational protein function prediction. Nat. Methods, 10, 221-227.
56. Rajamani,D. et al. (2004) Anchor residues in protein-protein interactions. Proc. Natl Acad. Sci. USA, 101, 11287-11292.
57. Rohl,C.A. et al. (2004) Protein structure prediction using Rosetta. Methods Enzymol., 383, 66-93.
58. Rother,M. et al. (2011) ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res., 39, 4007-4022.
59. Samish,I. (2009) Search and sampling in structural bioinformatics. In: Bourne,P.E. and Gu,J. (eds) Structural Bioinformatics. Wiley-Blackwell, New York, pp. 207-236.
60. Samish,I. et al. (2011) Theoretical and computational protein design. Annu. Rev. Phys. Chem., 62, 129-149.
61. Sandve,G.K. et al. (2013) Ten simple rules for reproducible computational research. PLoS Comput Biol., 9, e1003285.
62. Shaw,D.E. et al. (2009) Millisecond-scale molecular dynamics simulations on Anton. SC '09: Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis. Portland, OR. 14-20 Nov. 2009. doi: 10.1145/1654059.1654126. 1.
63. Shirts,M. and Pande,V.S. (2000) COMPUTING: screen savers of the world unite! Science, 290, 1903-1904.
64. Sillitoe,I. et al. (2013) New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res., 41, D490-D498.
65. Stein,M. et al. (2007) Bridging from molecular simulation to biochemical networks. Curr. Opin. Struct. Biol., 17, 166-172.
66. Tew,G.N. et al. (2010) De novo design of antimicrobial polymers, foldamers, and small molecules: from discovery to practical applications. Acc. Chem. Res., 43, 30-39.
67. Wang,Q. et al. (2008) SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. Nat. Protoc., 3, 1832-1847.
68. Wang,Y. et al. (2011) Implementation of accelerated molecular dynamics in NAMD. Comput. Sci. Discov., 4, 015002.
69. Warren,G.L. et al. (2006) A critical assessment of docking programs and scoring functions. J. Med. Chem., 49, 5912-5931.
70. Watson,J.D. and Crick,F.H. (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 171, 737-738.
71. Way,J.C. et al. (2014) Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell, 157, 151-161.
72. Winter,C. et al. (2012) Protein interactions in 3D: from interface evolution to drug discovery. J. Struct. Biol., 179, 347-358.
73. Wolynes,P.G. et al. (1995) Navigating the folding routes. Science, 267, 1619-1620.
74. Xie,L. et al. (2011a) Structure-based systems biology for analyzing off-target binding. Curr. Opin. Struct. Biol., 21, 189-199.
75. Xie,L. et al. (2011b) Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir. PLoS Comput. Biol., 7, e1002037.
76. Xie,L. et al. (2014) Towards structural systems pharmacology to study complex diseases and personalized medicine. PLoS Comput. Biol., 10, e1003554.
77. Yonath,A. (2010) Polar Bears, Antibiotics, and the Evolving Ribosome (Nobel Lecture). Wiley-VCH Verlag.