Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Fraccalvieri, Domenico ^a   Pandini, Alessandro ^b   Stella, Fabio ^a   Bonati, Laura ^a  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL ANALYSIS; CONFORMATIONAL DYNAMICS; CONFORMATIONAL ENSEMBLE; HIER-ARCHICAL CLUSTERING; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR DYNAMICS TRAJECTORIES; OPTIMAL SAMPLING RATES; TAGUCHI EXPERIMENTAL DESIGN;

CONFORMATIONS; MOLECULAR DYNAMICS; OPTIMIZATION; PROTEINS; TRAJECTORIES; VECTOR SPACES;

CLUSTERING ALGORITHMS;

PROTEIN; SPECTRIN;

ALGORITHM; ANIMAL; ARTICLE; CHEMISTRY; CHICKEN; GENETICS; MOLECULAR DYNAMICS; POINT MUTATION; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; ANIMALS; CHICKENS; MOLECULAR DYNAMICS SIMULATION; POINT MUTATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SPECTRIN;

EID: 79955827896     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-158     Document Type: Article

References (69)

1. Henzler-Wildman K, Kern D. Dynamic personalities of proteins. Nature 2007, 450:964-72. 10.1038/nature06522, 18075575.
2. Tokuriki N, Tawfik DS. Protein dynamism and evolvability. Science 2009, 324:203-7. 10.1126/science.1169375, 19359577.
3. Karplus M, Kuriyan J. Molecular dynamics and protein function. Proc Natl Acad Sci USA 2005, 102:6679-85. 10.1073/pnas.0408930102, 1100762, 15870208.
4. van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NFA, Yu HB. Biomolecular modeling: Goals, problems, perspectives. Angew Chem Int Ed Engl 2006, 45:4064-92. 10.1002/anie.200502655, 16761306.
5. Shao J, Tanner SW, Thompson N, Cheatham TE. Clustering molecular dynamics trajectories: 1. Characterizing the Performance of different clustering algorithms. J Chem Theory Comput 2007, 3:2312-2334.
6. Chodera JD, Singhal N, Pande VS, Dill K, Swope W. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys 2007, 126:155101. 10.1063/1.2714538, 17461665.
7. Noé F, Horenko I, Schütte C, Smith JC. Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States. J Chem Phys 2007, 126:155102. 10.1063/1.2714539, 17461666.
8. Muff S, Caflisch A. Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a b-sheet miniprotein. Proteins 2008, 70:1185-1195.
9. Huisinga W, Best C, Roitzsch R, Schütte C, Cordes F. From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods. J Comput Chem 1999, 20:1760-1774.
10. Deuflhard P, Huisinga W, Fischer A, Schutte C. Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains. Linear Alg Appl 2000, 315:39-59.
11. Keller B, Daura X, van Gunsteren WF. Comparing geometric and kinetic cluster algorithms for molecular simulation data. J Chem Phys 2010, 132:074110. 10.1063/1.3301140, 20170218.
12. Karpen ME, Tobias DJ, Brooks CL. Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV. Biochemistry 1993, 32:412-420. 10.1021/bi00053a005, 8422350.
13. Shenkin PS, McDonald DQ. Cluster analysis of molecular conformations. J Comput Chem 1994, 15:899-916.
14. Torda AE, van Gunsteren WF. Algorithms for clustering molecular dynamics configurations. J Comput Chem 1994, 15:1331-1340.
15. Pandini A, Bonati L. Conservation and specialization in PAS domain dynamics. Protein Eng Des Sel 2005, 18:127-137. 10.1093/protein/gzi017, 15820977.
16. Pang A, Arinaminpathy Y, Sansom MS, Biggin PC. Comparative molecular dynamics--similar folds and similar motions?. Proteins 2005, 61:809-22. 10.1002/prot.20672, 16231327.
17. Cascella M, Micheletti C, Rothlisberger U, Carloni P. Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases. J Am Chem Soc 2005, 127:3734-42. 10.1021/ja044608+, 15771507.
18. Pandini A, Mauri G, Bordogna A, Bonati L. Detecting similarities among distant homologous proteins by comparison of domain flexibilities. Protein Eng Des Sel 2007, 20:285-299. 10.1093/protein/gzm021, 17573407.
19. Maguid S, Fernandez-Alberti S, Echave J. Evolutionary conservation of protein vibrational dynamics. Gene 2008, 422:7-13. 10.1016/j.gene.2008.06.002, 18577430.
20. Velázquez-Muriel JA, Rueda M, Cuesta I, Pascual-Montano A, Orozco M, Carazo JM. Comparison of molecular dynamics and superfamily spaces of protein domain deformation. BMC Struct Biol 2009, 9:6. 10.1186/1472-6807-9-6, 2666742, 19220918.
21. Raimondi F, Orozco M, Fanelli F. Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily. Structure 2010, 18:402-14. 10.1016/j.str.2009.12.015, 20223222.
22. Kohonen T. The self-organizing map. Proceedings of the Institute of Electrical and Electronics Engineers 1990, 78:1464-1480.
23. Hyvönen MT, Hiltunen Y, El-Deredy W, Ojala T, Vaara J, Kovanen PT, Ala-Korpela M. Application of self-organizing maps in conformational analysis of lipids. J Am Chem Soc 2001, 123:810-806. 10.1021/ja0025853, 11456614.
24. Murtola T, Kupiainen M, Falck E, Vattulainen I. Conformational analysis of lipid molecules by self-organizing maps. J Chem Phys 2007, 126:054707. 10.1063/1.2429066, 17302498.
25. Bouvier G, Evrard-Todeschi N, Girault J-P, Bertho G. Automatic clustering of docking poses in virtual screening process using self-organizing map. Bioinformatics 2010, 26:53-60. 10.1093/bioinformatics/btp623, 19910307.
26. Vesanto J, Alhoniemi E. Clustering of the Self-Organizing Map. IEEE T Neural Network 2000, 11:586-600.
27. Xu R, Wunsch DC. Clustering 2009, Hoboken, New Jersey, John Wiley and Sons.
28. Li SS. Specificity and versatility of SH3 and other proline-recognition domains: structural basis and implications for cellular signal transduction. Biochem J 2005, 390:641-653. 1199657, 16134966.
29. Wang C, Pawley NH, Nicholson LK. The role of backbone motions in ligand binding to the c-Src SH3 domain. J Mol Biol 2001, 313:873-887. 10.1006/jmbi.2001.5083, 11697910.
30. Casares S, López-Mayorga O, Vega MC, Cámara-Artigas A, Conejero-Lara F. Cooperative propagation of local stability changes from low-stability and high-stability regions in a SH3 domain. Proteins 2007, 67:531-547. 10.1002/prot.21284, 17330285.
31. Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: A message-passing parallel molecular dynamics implementation. Comp Phys Comm 1995, 91:43-56.
32. Lindahl E, Hess B, van der Spoel D. Gromacs 3.0: A package for molecular simulation and trajectory analysis. J Mol Mod 2001, 7:306-317.
33. van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC. GROMACS: Fast, Flexible and Free. J Comput Chem 2005, 26:1701-1718. 10.1002/jcc.20291, 16211538.
34. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. Intermolecular Forces 1981, 331-342. Dordrecht, Reidel, Pullman B.
35. Darden T, York D, Pedersen L. Particle mesh Ewald: An N-log(N) method for Ewald sums in large Systems. J Chem Phys 1993, 98:10089-10092.
36. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh ewald potential. J Chem Phys 1995, 103:8577-8592.
37. Miyamoto S, Kollman PA. Settle: An analytical version of the shake and Rattle algorithms for rigid water models. J Comput Chem 1992, 13:952-962.
38. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM. LINCS: A linear constraint solver for molecular simulations. J Comput Chem 1997, 18:1463-1472.
39. Hess B. Similarities between principal components of protein dynamics and random diffusion. Phys Rev E 2000, 62:8438-8448.
40. Hess B. Convergence of sampling in protein simulations. Phys Rev E 2002, 65:031910/1-031910/10.
41. Amadei A, Linssen ABM, Berendsen HJC. Essential dynamics of proteins. Proteins 1993, 17:412-425. 10.1002/prot.340170408, 8108382.
42. Haykin S. Neural Networks: a comprehensive foundation 1999, Upper Saddle River, New Jersey, Prentice-Hall Inc.
43. Vesanto J, Himberg J, Alhonemi E, Parhankangas J. SOM Toolbox for Matlab 5 2000, Espoo, Libella Oy.
44. Wehrens R, Buydens LMC. Self- and Super-organising Maps in R: the kohonen package. J Stat Softw 2007, 21(5).
45. Kohonen T. Self-Organizing maps 2001, Gottingen, Springer, 3.
46. Chan CKK, Hsu AL, Tang SL, Halgamuge SK. Using Growing Self-Organizing Maps to Improve the Binning Process in Environmental Whole-Genome. J Biomed Biotechnol 2008, 2008:513701. 2235928, 18288261.
47. Newman AM, Cooper JB. AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. BMC Bioinformatics 2010, 11:117. 10.1186/1471-2105-11-117, 2846907, 20202218.
48. Raskutti B, Leckie C. An Evaluation of Criteria for Measuring the Quality of Clusters. Proceedings of the Sixteenth International Joint Conference on Artificial Intelligence 1999, 905-910.
49. Clarke B, Fokoué E, Zhang HH. Principles and theory for data mining and machine learning 2009, Dordrecht, Springer.
50. Douglas C, Montgomery DC. Design and Analysis of Experiments, Student Solutions Manual 2005, Wiley.
51. Box EP, Hunter WG, Hunter JS. Statistics for Experimenters: An Introduction to Design, Data Analysis, and Model Building 1978, John Wiley and Sons.
52. Juran J. Juran's Quality Control Handbook 1988, McGraw-Hill.
53. Roy R. Design of Experiments Using The Taguchi Approach: 16 Steps to Product and Process Improvement 2001, John Wiley and Sons.
54. Myers RH, Montgomery DC. Response Surface Methodology: Process and Product Optimization Using Designed Experiments 1995, Wiley Series in Probability and Statistics.
55. SAS Institute Inc JMP, Version 7 Cary, NC 1989, SAS Institute Inc.
56. Cressie N, Read TRC. Multinomial goodness-of-fit tests. J R Stat Soc Ser B 1984, 46:440-464.
57. Handbook of Psychology, Research Methods in Psychology 2003, 2. John Wiley and Sons, John A Schinka, Wayne F Velicer.
58. Mojena R. Hierarchical grouping methods and stopping rules: An evaluation. Comput J 1977, 4:359-363.
59. The Mathworks Inc Statistics Toolbox 7 User's Guide Natick, MA 1993, The Mathworks Inc.
60. Daura X, Gademann K, Jaun B, Seebach D, van Gunsteren WF, Mark AE. Peptide Folding: When Simulation Meets Experiment. Angew Chem Int Ed 1999, 38:236-240.
61. Rousseeuw PJ. Silhouettes: a Graphical Aid to the Interpretation and Validation of Cluster Analysis. Journal of Comp Appl Math 1987, 20:53-65.
62. Davies D, Bouldin D. A cluster separation measure. IEEE Trans Pattern Anal Mach Intelligence 1979, 1:224-227.
63. Kaufman L, Rousseeuw P. Finding Groups in Data 1990, Wiley, New York.
64. Musacchio A, Noble M, Pauptit R, Wierenga R, Saraste M. Crystal structure of a Src-homology 3 (SH3) domain. Nature 1992, 359:851-855. 10.1038/359851a0, 1279434.
65. Casares S, AB E, Eshuis H, López-Mayorga O, van Nuland NAJ, Conejero-Lara F. The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: Understanding the determinants of binding affinity by comparison with Abl-SH3. BMC Struct Biol 2007, 7:22. 10.1186/1472-6807-7-22, 1853097, 17407569.
66. Fernandez-Ballester G, Beltrao P, Gonzales JM, Song Y, Wilmanns M, Valencia A, Serrano L. Structure-based prediction of the saccharomyces cerevisiae SH3-ligand interactions. J Mol Biol 2009, 388:902-916. 10.1016/j.jmb.2009.03.038, 19324052.
67. Vega MC, Martinez JC, Serrano L. Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II' region of the Ramachandran plot. Protein Sci 2000, 9:2322-2328. 10.1110/ps.9.12.2322, 2144520, 11206053.
68. Faraldo-Gomez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cuthbertson J, Sansom MSP. Conformational Sampling and Dynamics of Membrane Proteins From 10-Nanosecond Computer Simulations. Proteins 2004, 57:783-791. 10.1002/prot.20257, 15317024.
69. Casares S, Sadqi M, López-Mayorga O, Martìnez JC, Conejero-Lara F. Structural cooperativity in the SH3 domain studied by site-directed mutagenesis and amide hydrogen exchange. FEBS Lett 2003, 539:125-130. 10.1016/S0014-5793(03)00212-6, 12650939.