PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data

Journal of Chemical Theory and Computation

Volumn 9, Issue 7, 2013, Pages 3084-3095

  Roe, Daniel R ^a   Cheatham, Thomas E ^a  

^a UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84880022273     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct400341p     Document Type: Article

References (40)

1. Klepeis, J. L.; Lindorff-Larsen, K.; Dror, R. O.; Shaw, D. E. Long-timescale molecular dynamics simulations of protein structure and function Curr. Opin. Struct. Biol. 2009, 19 (2) 120-127
2. Durrant, J. D.; McCammon, J. A. Molecular dynamics simulations and drug discovery BMC Biol. 2011, 9, 71
3. Schlick, T.; Collepardo-Guevara, R.; Halvorsen, L. A.; Jung, S.; Xiao, X. Biomolecularmodeling and simulation: a field coming of age Q. Rev. Biophys. 2011, 44 (2) 191-228
4. Wereszczynski, J.; McCammon, J. A. Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition Q. Rev. Biophys. 2012, 45 (1) 1-25
5. Perez, A.; Luque, F. J.; Orozco, M. Frontiers in molecular dynamics simulations of DNA Acc. Chem. Res. 2012, 45 (2) 196-205
6. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; Debolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structure and energetic properties of molecules Comput. Phys. Commun. 1995, 91 (1-3) 1-41
7. Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber biomolecular simulation programs J. Comput. Chem. 2005, 26 (16) 1668-1688 (Pubitemid 43076180)
8. Humphrey, W.; Dalke, A.; Schulten, K. VMD-Visual Molecular Dynamics J. Mol. Graphics Modell. 1996, 14, 33-38
9. Feig, M.; Karanicolas, J.; Brooks, C. L., III. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology J. Mol. Graphics Modell. 2001, 22 (5) 377-395 (Pubitemid 38510304)
10. Michaud-Agrawal, N.; Denning, E. J.; Woolf, T. B.; Beckstein, O. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations J. Comput. Chem. 2011, 32, 2319-2327
11. Yesylevskyy, S. O. Pteros: Fast and Easy to Use Open-Source C++ Library for Molecular Analysis J. Comput. Chem. 2012, 33, 1632-1636
12. Romo, T. D.; Grossfield, A. LOOS: An extensible platform for the structural analysis of simulations. In 31st Annual International Conference of the IEEE EMBS; IEEE: New York, 2009; pp 2332-2335.
13. Tu, T.; Rendleman, C. A.; Borhani, D. W.; Dror, R. O.; Gullingsrud, J.; Jensen, M. Ø.; Klepeis, J. L.; Maragakis, P.; Miller, P.; Stafford, K. A.; Shaw, D. E. A Scalable Parallel Framework for Analyzing Terascale Molecular Dynamics Simulation Trajectories. In Proceedings of the ACM/IEEE Conference on Supercomputing (SC08), Austin, TX, November 15-21, 2008; IEEE: New York: 2008; pp 15-21.
14. Brooks, B. R.; Brooks, C. L., III; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: the biomolecular simulation program J. Comput. Chem. 2009, 30 (10) 1545-1614
15. Dagum, L.; Menon, R. OpenMP: An Industry-Standard API for Shared-Memory Programming IEEE Comput. Sci. Eng. 1998, 5 (1) 46-55
16. Weiser, J.; Shenkin, P. S.; Still, W. C. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) J. Comput. Chem. 1999, 20, 217-230 (Pubitemid 129653030)
17. Altona, C.; Sundaralingam, M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation J. Am. Chem. Soc. 1972, 94 (23) 8205-8212
18. Harvey, S. C.; Prabhakaran, M. Ribose puckering-structure, dynamics, energetics, and the pseudorotation cycle J. Am. Chem. Soc. 1986, 108, 6128-6136
19. Cremer, D.; Pople, J. A. A general definition of ring puckering coordinates J. Am. Chem. Soc. 1975, 97, 1354-1358
20. Kabsch, W. A discussion of the solution for the best rotation to relate two sets of vectors Acta Crystallogr., Sect. A 1978, 34, 827-828
21. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22 (12) 2577-2637
22. Miller, B. R., III; McGee, T. D., Jr.; Swails, J. M.; Homeyer, N.; Gohlke, H.; Roitberg, A. E. MMPBSA.py: An efficient program for end-state free energy calculations J. Chem. Theory Comput. 2012, 8, 3314-3321
23. Prompers, J. J.; Bruschweiler, R. General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation J. Am. Chem. Soc. 2002, 124 (16) 4522-4534 (Pubitemid 34441586)
24. Prompers, J. J.; Bruschweiler, R. Dynamic and structural analysis of isotropically distributed molecular ensembles Proteins 2002, 46 (2) 177-189 (Pubitemid 34052071)
25. Anderson, E.; Bai, Z.; Bischof, C.; Blackford, J.; Demmel, J.; Dongara, J.; Du Croz, J.; Greenbaum, A.; Hammarling, S.; McKenney, A.; Sorensen, D. C. LAPACK Users' Guide, 3 rd ed.; SIAM: Philadelphia, PA, 1999.
26. Lehoucq, R. B.; Sorensen, D. C.; Yang, C. ARPACK Users' Guide: Solution of Large-Scale Eigenvalue Problems with Implicitly Restarted Arnoldi Methods; SIAM: Philadelphia, PA, 1998.
27. Abseher, R.; Nilges, M. Are there non-trivial dynamic cross-correlations in proteins? J. Mol. Biol. 1998, 279 (4) 911-920 (Pubitemid 28284705)
28. Shao, J.; Tanner, S. W.; Thompson, N.; Cheatham, T. E., III. Clustering molecular dynamics trajectories. 1. Characterizing the performance of different clustering algorithms J. Chem. Theory Comput. 2007, 3, 2312-2334
29. Connolly, M. L. Solvent-accessible surfaces of proteins and nucleic acids Science 1983, 221 (4612) 709-713
30. Connolly, M. Analytical molecular surface calculation J. Appl. Crystallogr. 1983, 16, 548-558
31. Chou, J. J.; Case, D. A.; Bax, A. Insights into the mobility of methyl-bearing side chains in proteins J. Am. Chem. Soc. 2003, 125, 8959-8966
32. Perez, C.; Lohr, F.; Ruterjans, H.; Schmidt, J. M. Self-consistent Karplus parametrization of 3J couplings depending on the polypeptide side-chain torsion chi1 J. Am. Chem. Soc. 2001, 123 (29) 7081-7093 (Pubitemid 32879499)
33. Lu, X. J.; Olson, W. K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures Nucleic Acids Res. 2003, 31 (17) 5108-5121 (Pubitemid 37441878)
34. Babcock, M. S.; Pednault, E. P.; Olson, W. K. Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures J. Mol. Biol. 1994, 237 (1) 125-156
35. Olson, W. K.; Bansal, M.; Burley, S. K.; Dickerson, R. E.; Gerstein, M.; Harvey, S. C.; Heinemann, U.; Lu, X. J.; Neidle, S.; Shakked, Z.; Sklenar, H.; Suzuki, M.; Tung, C. S.; Westhof, E.; Wolberger, C.; Berman, H. M. A standard reference frame for the description of nucleic acid base-pair geometry J. Mol. Biol. 2001, 313 (1) 229-237 (Pubitemid 33001177)
36. Wong, V.; Case, D. A. Evaluating rotational diffusion from protein MD simulations J. Phys. Chem. B 2008, 112 (19) 6013-6024
37. Raymond, J. W.; Willett, P. Maximum common subgraph isomorphism algorithms for the matching of chemical structures J. Comput.-Aided Mol. Des. 2002, 16 (7) 521-533 (Pubitemid 36013605)
38. Brozell, S. R.; Mukherjee, S.; Balius, T. E.; Roe, D. R.; Case, D. A.; Rizzo, R. C. Evaluation of DOCK 6 as a pose generation and database enrichment tool J. Comput.-Aided Mol. Des. 2012, 26 (6) 749-773
39. Bacon, D. F.; Graham, S. L.; Sharp, O. J. Compiler transformations for high-performance computing ACM Comput. Surv. 1994, 26, 345-420
40. Geist, A.; Gropp, W.; Huss-Lederman, S.; Lumsdaine, A.; Lusk, E.; Saphir, W.; Skjellum, T.; Snir, M. MPI-2: Extending the message-passing interface. In Euro-Par'96 Parallel Processing Lecture Notes in Computer Science; Springer: New York, 1996; pp 128-135. (Pubitemid 126116035)