Home LiteratureArticle Details
PMID: 25488929 Published · ppublish English Journal Article

Achievements and challenges in structural bioinformatics and computational biophysics.

Bioinformatics (Oxford, England) ·Vol. 31 ·No. 1 ·2015-01-01 ·Pages 146-50

Samish I, Bourne PE, Najmanovich RJ

Abstract

The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects. An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results. The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field.

MeSH Terms
Achievement Biomedical Research/trends Biophysics/trends Computational Biology/trends Humans
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Samish Ilan
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada.
Bourne Philip E
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada.
Najmanovich Rafael J
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada.
References (73)
73 references, click to expand
  1. Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm.
    PLoS Comput Biol. 2010 Mar 05;6(3):e1000694 PMID: 20221255
  2. Bridging from molecular simulation to biochemical networks.
    Curr Opin Struct Biol. 2007 Apr;17(2):166-72 PMID: 17395455
  3. Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis.
    PLoS Comput Biol. 2009 Jul;5(7):e1000423 PMID: 19578428
  4. Computational enzyme design.
    Angew Chem Int Ed Engl. 2013 May 27;52(22):5700-25 PMID: 23526810
  5. Computational approaches to 3D modeling of RNA.
    J Phys Condens Matter. 2010 Jul 21;22(28):283101 PMID: 21399271
  6. Computational redesign of a protein-protein interface for high affinity and binding specificity using modular architecture and naturally occurring template fragments.
    J Mol Biol. 2008 Dec 5;384(1):109-19 PMID: 18804117
  7. Predicting protein structures with a multiplayer online game.
    Nature. 2010 Aug 5;466(7307):756-60 PMID: 20686574
  8. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.
    Nature. 1953 Apr 25;171(4356):737-8 PMID: 13054692
  9. Protein interactions in 3D: from interface evolution to drug discovery.
    J Struct Biol. 2012 Sep;179(3):347-58 PMID: 22595401
  10. Theoretical and computational protein design.
    Annu Rev Phys Chem. 2011;62:129-49 PMID: 21128762
  11. COMPUTING: Screen Savers of the World Unite!
    Science. 2000 Dec 8;290(5498):1903-4 PMID: 17742054
  12. New faster CHARMM molecular dynamics engine.
    J Comput Chem. 2014 Feb 15;35(5):406-13 PMID: 24302199
  13. Anchor residues in protein-protein interactions.
    Proc Natl Acad Sci U S A. 2004 Aug 3;101(31):11287-92 PMID: 15269345
  14. The birth of computational structural biology.
    Nat Struct Biol. 2001 May;8(5):392-3 PMID: 11323711
  15. SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling.
    Nat Protoc. 2008;3(12):1832-47 PMID: 18989261
  16. Developments in the CCP4 molecular-graphics project.
    Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2288-94 PMID: 15572783
  17. Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations.
    Parallel Comput. 2014 May 1;40(5-6):86-99 PMID: 24882911
  18. From Levinthal to pathways to funnels.
    Nat Struct Biol. 1997 Jan;4(1):10-9 PMID: 8989315
  19. The Levinthal paradox: yesterday and today.
    Fold Des. 1997;2(4):S69-75 PMID: 9269572
  20. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
    Bioinformatics. 2013 Apr 1;29(7):845-54 PMID: 23407358
  21. 3D-Jury: a simple approach to improve protein structure predictions.
    Bioinformatics. 2003 May 22;19(8):1015-8 PMID: 12761065
  22. ModeRNA: a tool for comparative modeling of RNA 3D structure.
    Nucleic Acids Res. 2011 May;39(10):4007-22 PMID: 21300639
  23. Protein structure prediction using Rosetta.
    Methods Enzymol. 2004;383:66-93 PMID: 15063647
  24. MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale.
    J Chem Theory Comput. 2011 Oct 11;7(10):3412-3419 PMID: 22125474
  25. Implementation of Accelerated Molecular Dynamics in NAMD.
    Comput Sci Discov. 2011;4(1): PMID: 21686063
  26. The Protein Data Bank.
    Nucleic Acids Res. 2000 Jan 1;28(1):235-42 PMID: 10592235
  27. WeFold: a coopetition for protein structure prediction.
    Proteins. 2014 Sep;82(9):1850-68 PMID: 24677212
  28. Macromolecular crowding and molecular recognition.
    J Mol Recognit. 1993 Dec;6(4):211-4 PMID: 7917416
  29. Principles of docking: An overview of search algorithms and a guide to scoring functions.
    Proteins. 2002 Jun 1;47(4):409-43 PMID: 12001221
  30. IsoCleft Finder - a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities.
    F1000Res. 2013 Apr 30;2:117 PMID: 24555058
  31. Accelerating molecular dynamic simulation on graphics processing units.
    J Comput Chem. 2009 Apr 30;30(6):864-72 PMID: 19191337
  32. Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis.
    Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):E1540-7 PMID: 22645369
  33. Polar bears, antibiotics, and the evolving ribosome (Nobel Lecture).
    Angew Chem Int Ed Engl. 2010 Jun 14;49(26):4341-54 PMID: 20535730
  34. Flexible backbone sampling methods to model and design protein alternative conformations.
    Methods Enzymol. 2013;523:61-85 PMID: 23422426
  35. Integrating biological redesign: where synthetic biology came from and where it needs to go.
    Cell. 2014 Mar 27;157(1):151-61 PMID: 24679533
  36. Principles of protein-protein recognition.
    Nature. 1975 Aug 28;256(5520):705-8 PMID: 1153006
  37. Towards a computational model of a methane producing archaeum.
    Archaea. 2014 Mar 04;2014:898453 PMID: 24729742
  38. Protein structure modeling with MODELLER.
    Methods Mol Biol. 2008;426:145-59 PMID: 18542861
  39. Assembly reflects evolution of protein complexes.
    Nature. 2008 Jun 26;453(7199):1262-5 PMID: 18563089
  40. Pfam: the protein families database.
    Nucleic Acids Res. 2014 Jan;42(Database issue):D222-30 PMID: 24288371
  41. Navigating the folding routes.
    Science. 1995 Mar 17;267(5204):1619-20 PMID: 7886447
  42. CAPRI: a Critical Assessment of PRedicted Interactions.
    Proteins. 2003 Jul 1;52(1):2-9 PMID: 12784359
  43. Towards structural systems pharmacology to study complex diseases and personalized medicine.
    PLoS Comput Biol. 2014 May 15;10(5):e1003554 PMID: 24830652
  44. 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. 2014 Apr 24;10(4):e1003569 PMID: 24762569
  45. Critical assessment of methods of protein structure prediction (CASP)--round x.
    Proteins. 2014 Feb;82 Suppl 2:1-6 PMID: 24344053
  46. The proteasome: structure, function, and role in the cell.
    Cancer Treat Rev. 2003 May;29 Suppl 1:3-9 PMID: 12738238
  47. New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D490-8 PMID: 23203873
  48. CASP and CAFASP experiments and their findings.
    Methods Biochem Anal. 2003;44:501-7 PMID: 12647401
  49. Determining RNA three-dimensional structures using low-resolution data.
    J Struct Biol. 2012 Sep;179(3):252-60 PMID: 22387042
  50. Macromolecular crowding: an important but neglected aspect of the intracellular environment.
    Curr Opin Struct Biol. 2001 Feb;11(1):114-9 PMID: 11179900
  51. Coarse-grained normal mode analysis in structural biology.
    Curr Opin Struct Biol. 2005 Oct;15(5):586-92 PMID: 16143512
  52. Protein structure prediction and structural genomics.
    Science. 2001 Oct 5;294(5540):93-6 PMID: 11588250
  53. Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges.
    Structure. 2014 Aug 5;22(8):1120-1139 PMID: 25066135
  54. De novo design of antimicrobial polymers, foldamers, and small molecules: from discovery to practical applications.
    Acc Chem Res. 2010 Jan 19;43(1):30-9 PMID: 19813703
  55. Structure-based systems biology for analyzing off-target binding.
    Curr Opin Struct Biol. 2011 Apr;21(2):189-99 PMID: 21292475
  56. Lessons from the lysozyme of phage T4.
    Protein Sci. 2010 Apr;19(4):631-41 PMID: 20095051
  57. Ten simple rules for cultivating open science and collaborative R&D.
    PLoS Comput Biol. 2013;9(9):e1003244 PMID: 24086123
  58. Data growth and its impact on the SCOP database: new developments.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D419-25 PMID: 18000004
  59. Protein 3D structure computed from evolutionary sequence variation.
    PLoS One. 2011;6(12):e28766 PMID: 22163331
  60. Ten simple rules for reproducible computational research.
    PLoS Comput Biol. 2013 Oct;9(10):e1003285 PMID: 24204232
  61. Principles of protein-protein interactions.
    Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):13-20 PMID: 8552589
  62. Docking and scoring in virtual screening for drug discovery: methods and applications.
    Nat Rev Drug Discov. 2004 Nov;3(11):935-49 PMID: 15520816
  63. Drug off-target effects predicted using structural analysis in the context of a metabolic network model.
    PLoS Comput Biol. 2010 Sep 23;6(9):e1000938 PMID: 20957118
  64. Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
    Bioinformatics. 2008 Aug 15;24(16):i105-11 PMID: 18689810
  65. Molecular recognition and docking algorithms.
    Annu Rev Biophys Biomol Struct. 2003;32:335-73 PMID: 12574069
  66. Enzyme (re)design: lessons from natural evolution and computation.
    Curr Opin Chem Biol. 2009 Feb;13(1):10-8 PMID: 19237310
  67. The pyruvate dehydrogenase complexes: structure-based function and regulation.
    J Biol Chem. 2014 Jun 13;289(24):16615-23 PMID: 24798336
  68. Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir.
    PLoS Comput Biol. 2011 Apr;7(4):e1002037 PMID: 21552547
  69. Prediction of protein function from structure: insights from methods for the detection of local structural similarities.
    Biotechniques. 2005 Jun;38(6):847, 849, 851 PMID: 16018542
  70. A critical assessment of docking programs and scoring functions.
    J Med Chem. 2006 Oct 5;49(20):5912-31 PMID: 17004707
  71. Molecular dynamics: survey of methods for simulating the activity of proteins.
    Chem Rev. 2006 May;106(5):1589-615 PMID: 16683746
  72. Computational design tools for synthetic biology.
    Curr Opin Biotechnol. 2009 Aug;20(4):479-85 PMID: 19758796
  73. A large-scale evaluation of computational protein function prediction.
    Nat Methods. 2013 Mar;10(3):221-7 PMID: 23353650
Article Info
Journal
Bioinformatics (Oxford, England)
Abbr.
Bioinformatics
ISSN
1367-4811
Published
2015-01-01
Epub
2014-00-08
Pages
146-50
Language
English
Region
England
NLM ID
9808944
PMCID
PMC4271151
Subset
IM
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com