Wordom: A user‐friendly program for the analysis of molecular structures, trajectories, and free energy surfaces

Abstract

Wordom is a versatile, user‐friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have been added since the publication of the original Wordom paper in 2007: assignment of secondary structure, calculation of solvent accessible surfaces, elastic network model, motion cross correlations, protein structure network, shortest intra‐molecular and inter‐molecular communication paths, kinetic grouping analysis, and calculation of mincut‐based free energy profiles. In addition, an interface with the Python scripting language has been built and the overall performance and user accessibility enhanced. The source code of Wordom (in the C programming language) as well as documentation for usage and further development are available as an open source package under the GNU General Purpose License from http://wordom.sf.net . © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

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References 62

1. 1.

   Seeber M, Cecchini M, Rao F, Settanni G, Caflisch A. Bioinformatics. 2007;23:2625.

   Not in our library10.1093/bioinformatics/btm378

2. 2.

   Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. J Comput Chem. 1983;4:187.

   Not in our library

3. 3.

   Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. J Comput Chem. 2009;30:1545.

   Not in our library10.1002/jcc.21287

4. 4.

   Lindahl E, Hess B, van der Spoel D. J Mol Model. 2001;7:306.

   Not in our library

5. 5.

   Case D, Cheatham T, Darden T, Gohlke H, Luo R, Merz K, Onufriev A, Simmerling C, Wang B, Woods R. J Comput Chem. 2005;26:1668.

   Not in our library10.1002/jcc.20290

6. 6.

   Case D, Darden T, Cheatham T, Simmerling C, Wang J, Duke R, Luo R, Walker R, Zhang W, Merz K, Roberts B, Wang B, Hayik S, Roitberg A, Seabra G, Kolossvry I, Wong K, Paesani F, Vanicek J, Wu X, Brozell S, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh M-J, Cui G, Roe D, Mathews D, Seetin M, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman P. 2010.

   Not in our library

7. 7.

   Humphrey W, Dalke A, Schulten K. J Mol Graphics. 1996;14:33.

   Not in our library10.1016/0263-7855(96)00018-5

8. 8.

   DeLano W. The PyMOL Molecular Graphics System. 2002.

   Not in our library

9. 9.

   Feig M, Karanicolas J, Brooks C. J Mol Graph Model. 2004;22:377.

   Not in our library10.1016/j.jmgm.2003.12.005

10. 10.

    Glykos N. J Comput Chem. 2006;27:1765.

    Not in our library10.1002/jcc.20482

11. 11.

    Meyer T, Ferrer-Costa C, Perez A, Rueda M, Bidon-Chanal A, Luque F, Laughton C, Orozco M. J Chem Theory Comput. 2006;2:251.

    Not in our library10.1021/ct050285b

12. 12.

    Grant B, Rodrigues A, ElSawy K, McCammon J, Caves L. Bioinformatics. 2006;22:2695.

    Not in our library10.1093/bioinformatics/btl461

13. 13.

    Hinsen K. J Comput Chem. 2000;21:79.

    Not in our library

14. 14.

    Grunberg R, Nilges M, Leckner J. Bioinformatics. 2007;23:769.

    Not in our library10.1093/bioinformatics/btl655

15. 15.

    Andersen CAF, Palmer AG, Brunak S, Rost B. Structure. 2002;10:174.

    Not in our library10.1016/s0969-2126(02)00700-1

16. 16.

    Carter P, Andersen C, Rost B. Nucleic Acids Res. 2003;31:3293.

    Not in our library10.1093/nar/gkg626

17. 17.

    Buša J, Džurina J, Hayryan E, Hayryan S, Hu C, Plavka J, Pokornỳ I, Skřivánek J, Wu M. Comput Phys Commun. 2005;165:59.

    Not in our library

18. 18.

    Pascual-Ahuir J, Silla E, Tunon I. J Comput Chem. 1994;15:1127.

    Not in our library

19. 19.

    Tirion M. Phys Rev Lett. 1996;77:1905.

    Not in our library10.1103/physrevlett.77.1905

20. 20.

    Delarue M, Sanejouand Y. J Mol Biol. 2002;320:1011.

    Not in our library10.1016/s0022-2836(02)00562-4

21. 21.

    Kovacs J, Chacón P, Abagyan R. Proteins. 2004;56:661.

    Not in our library10.1002/prot.20151

22. 22.

    Zheng W, Brooks B, Doniach S, Thirumalai D. Structure. 2005;13:565.

    Not in our library10.1016/j.str.2005.01.017

23. 23.

    Bahar I, Atilgan A, Erman B. Fold Des. 1997;2:173.

    Not in our library10.1016/s1359-0278(97)00024-2

24. 24.

    Marques O, Sanejouand Y. Proteins. 1995;23:557.

    Not in our library10.1002/prot.340230410

25. 25.

    McCammon JA, Harvey S. Dynamics of Proteins and Nucleic Acids. 1987.

    Not in our library

26. 26.

    Kraskov A, Stoegbauer H, Grassberger P. Phys Rev E. 2004;69:66138.

    Not in our library10.1103/physreve.69.066138

27. 27.

    Lange O, Grubmuller H. Proteins. 2006;62:1053.

    Not in our library10.1002/prot.20784

28. 28.

    Kannan N, Vishveshwara S. J Mol Biol. 1999;292:441.

    Not in our library10.1006/jmbi.1999.3058

29. 29.

    Brinda KV, Vishveshwara S. Biophys J. 2005;89:4159.

    Not in our library10.1529/biophysj.105.064485

30. 30.

    Vishveshwara S, Ghosh A, Hansia P. Curr Protein Pept Sci. 2009;10:146.

    Not in our library10.2174/138920309787847590

31. 31.

    del Sol A, Fujihashi H, Amoros D, Nussinov R. Mol Syst Biol. 2006;2:2006.0019.

    Not in our library10.1038/msb4100063

32. 32.

    Ghosh A, Vishveshwara S. Proc Natl Acad Sci USA. 2007;104:15711.

    Not in our library10.1073/pnas.0704459104

33. 33.

    Dijkstra E. Numer Math. 1959;1:269.

    Not in our library

34. 34.

    Hartigan J. Clustering Algorithms. 1975.

    Not in our library

35. 35.

    Johnson S. Psychometrika. 1967;32:241.

    Not in our library10.1007/bf02289588

36. 36.

    Heyer L, Kruglyak S, Yooseph S. Genome Res. 1999;9:1106.

    Not in our library10.1101/gr.9.11.1106

37. 37.

    del Sol A, O'Meara P. Proteins. 2005;58:672.

    Not in our library10.1002/prot.20348

38. 38.

    Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, Venger I, Pietrokovski S. J Mol Biol. 2004;344:1135.

    Not in our library10.1016/j.jmb.2004.10.055

39. 39.

    Krivov SV, Muff S, Caflisch A, Karplus M. J Phys Chem B. 2008;112:8701.

    Not in our library10.1021/jp711864r

40. 40.

    Muff S, Caflisch A. Proteins. 2008;70:1185.

    Not in our library10.1002/prot.21565

41. 41.

    Suhre K, Sanejouand Y. Nucleic Acids Res. 2004;32(Web Server Issue):W610.

    Not in our library10.1093/nar/gkh368

42. 42.

    Eyal E, Yang L, Bahar I. Bioinformatics. 2006;22:2619.

    Not in our library10.1093/bioinformatics/btl448

43. 43.

    Zheng W. AD-ENM Web Server. 2010.

    Not in our library

44. 44.

    Lindahl E, Azuara C, Koehl P, Delarue M. Nucleic Acids Res. 2006;34(Web Server issue):W52.

    Not in our library10.1093/nar/gkl082

45. 45.

    Hollup S, Salensminde G, Reuter N. BMC Bioinformatics. 2005;6:52.

    Not in our library10.1186/1471-2105-6-52

46. 46.

    Krivov SV, Karplus M. J Phys Chem B. 2006;110:12689.

    Not in our library10.1021/jp060039b

47. 47.

    Vendruscolo M, Dokholyan N, Paci E, Karplus M. Phys Rev E. 2002;65:61910.

    Not in our library10.1103/physreve.65.061910

48. 48.

    Paoli B, Pellarin R, Caflisch A. J Phys Chem B. 2010;114:2023.

    Not in our library10.1021/jp910216j

49. 49.

    Kabsch W, Sander C. Biopolymers. 1983;22:2577.

    Not in our library10.1002/bip.360221211

50. 50.

    Orengo C, Michie A, Jones S, Jones D, Swindells M, Thornton J. Structure. 1997;5:1093.

    Not in our library10.1016/s0969-2126(97)00260-8

51. 51.

    Van Wynsberghe A, Cui Q. Structure. 2006;14:1647.

    Not in our library10.1016/j.str.2006.09.003

52. 52.

    Muff S, Caflisch A. J Chem Phys. 2009;130:125104.

    Not in our library10.1063/1.3099705

53. 53.

    Rao F, Caflisch A. J Mol Biol. 2004;342:299.

    Not in our library10.1016/j.jmb.2004.06.063

54. 54.

    Rao F, Settanni G, Guarnera E, Caflisch A. J Chem Phys. 2005;122:184901.

    Not in our library10.1063/1.1893753

55. 55.

    Ihalainen J, Paoli B, Muff S, Backus E, Bredenbeck J, Woolley G, Caflisch A, Hamm P. Proc Natl Acad Sci USA. 2008;105:9588.

    Not in our library10.1073/pnas.0712099105

56. 56.

    Paoli B, Seeber M, Backus E, Ihalainen J, Hamm P, Caflisch A. J Phys Chem B. 2009;113:4435.

    Not in our library10.1021/jp810431s

57. 57.

    Yew Z, Krivov S, Paci E. J Phys Chem B. 2008;112:16902.

    Not in our library10.1021/jp807316e

58. 58.

    Gfeller D, De Los Rios P, Caflisch A, Rao F. Proc Natl Acad Sci USA. 2007;104:1817.

    Not in our library10.1073/pnas.0608099104

59. 59.

    Gfeller D, de Lachapelle DM, De Los Rios P, Caldarelli G, Rao F. Phys Rev E. 2007;76:026113.

    Not in our library10.1103/physreve.76.026113

60. 60.

    Gomory R, Hu T. SIAM J Appl Math. 1961;9:551.

    Not in our library

61. 61.

    Krivov S, Karplus M. Proc Natl Acad Sci USA. 2004;101:14766.

    Not in our library10.1073/pnas.0406234101

62. 62.

    Beazley D. The Simple Wrapper and Interface Generator.

    Not in our library

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