ISOLDE: A physically realistic environment for model building into low-resolution electron-density maps

Acta Crystallographica Section D: Structural Biology

Volumn 74, Issue 6, 2018, Pages 519-530

  Croll, Tristan Ian ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

ISOLDE; Model building; Molecular dynamics; Real space refinement; Visualization

Indexed keywords

FUNGAL PROTEIN; MINICHROMOSOME MAINTENANCE PROTEIN;

CHEMISTRY; COMPUTER SIMULATION; CRYOELECTRON MICROSCOPY; MACROMOLECULE; MEASUREMENT ACCURACY; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROCEDURES; SOFTWARE; VALIDATION STUDY;

COMPUTER SIMULATION; CRYOELECTRON MICROSCOPY; DATA ACCURACY; FUNGAL PROTEINS; MACROMOLECULAR SUBSTANCES; MINICHROMOSOME MAINTENANCE PROTEINS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; SOFTWARE; VALIDATION STUDIES AS TOPIC;

EID: 85048328149     PISSN: None     EISSN: 20597983     Source Type: Journal    
DOI: 10.1107/S2059798318002425     Document Type: Article

References (46)

1. Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221.
2. Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. & Adams, P. D. (2012). Acta Cryst. D68, 352-367.
3. Afonine, P. V., Klaholz, B. P., Moriarty, N. W., Poon, B. K., Sobolev, O. V., Terwilliger, T. C., Adams, P. D. & Urzhumtsev, A. (2018). bioRxiv, https://doi.org/10.1101/279844.
4. Brändén, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689.
5. Brereton, A. E. & Karplus, P. A. (2016). Protein Sci. 25, 926-932.
6. Brünger, A. T. (1992). X-PLOR Version 3.1. A System for X-ray Crystallography and NMR. New Haven: Yale University Press.
7. Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12-21.
8. Chen, V. B., Davis, I. W. & Richardson, D. C. (2009). Protein Sci. 18, 2403-2409.
9. Conti, F., Barbagli, F., Balaniuk, R., Halg, M., Lu, C., Morris, D., Sentis, L., Vileshin, E., Warren, J., Khatib, O. & Salisbury, K. (2003). EuroHaptics 2003: Proceedings, edited by I. Oakley, S. O’Modhrain & F. Newell, pp. 496-500. Dublin: Media Lab.
10. Cowtan, K. (2006). Acta Cryst. D62, 1002-1011.
11. Croll, T. I. (2015). Acta Cryst. D71, 706-709.
12. Croll, T. I. & Andersen, G. R. (2016). Acta Cryst. D72, 1006-1016.
13. Croll, T. I., Smith, B. J., Margetts, M. B., Whittaker, J., Weiss, M. A., Ward, C. W. & Lawrence, M. C. (2016). Structure, 24, 469-476.
14. Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., Wiewiora, R. P., Brooks, B. R. & Pande, V. S. (2017). PLoS Comput. Biol. 13, e1005659.
15. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
16. Focht, D., Croll, T. I., Pedersen, B. P. & Nissen, P. (2017). Front. Physiol. 8, 202.
17. Goddard, T. D., Huang, C. C., Meng, E. C., Pettersen, E. F., Couch, G. S., Morris, J. H. & Ferrin, T. E. (2017). Protein Sci. 27, 14-25.
18. Hintze, B. J., Lewis, S. M., Richardson, J. S. & Richardson, D. C. (2016). Proteins, 84, 1177-1189.
19. Hooft, R.W.W., Vriend, G., Sander, C. & Abola, E. E. (1996). Nature (London), 381, 272.
20. Joosten, R. P., Joosten, K., Murshudov, G. N. & Perrakis, A. (2012). Acta Cryst. D68, 484-496.
21. Joosten, R. P., Long, F., Murshudov, G. N. & Perrakis, A. (2014). IUCrJ, 1, 213-220.
22. Joseph, A. P., Malhotra, S., Burnley, T., Wood, C., Clare, D. K., Winn, M. & Topf, M. (2016). Methods, 100, 42-49.
23. Kirmizialtin, S., Loerke, J., Behrmann, E., Spahn, C. M. T. & Sanbonmatsu, K. Y. (2015). Methods Enzymol. 558, 497-514.
24. Kleywegt, G. J. (2000). Acta Cryst. D56, 249-265.
25. Kleywegt, G. J. & Jones, T. A. (1995). Structure, 3, 535-540.
26. Langer, G., Cohen, S. X., Lamzin, V. S. & Perrakis, A. (2008). Nature Protoc. 3, 1171-1179.
27. Laskowski, R. A., MacArthur, M. W. & Thornton, J. M. (1998). Curr. Opin. Struct. Biol. 8, 631-639.
28. Li, P., Song, L. F. & Merz, K. M. Jr (2015). J. Phys. Chem. B, 119, 883-895.
29. Li, N., Zhai, Y., Zhang, Y., Li, W., Yang, M., Lei, J., Tye, B.-K. & Gao, N. (2015). Nature (London), 524, 186-191.
30. Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E. & Simmerling, C. (2015). J. Chem. Theory Comput. 11, 3696-3713.
31. McNicholas, S., Croll, T., Burnley, T., Palmer, C. M., Hoh, S. W., Jenkins, H. T., Dodson, E., Cowtan, K. & Agirre, J. (2017). Protein Sci. 27, 207-216.
32. McNicholas, S., Potterton, E., Wilson, K. S. & Noble, M. E. M. (2011). Acta Cryst. D67, 386-394.
33. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355-367.
34. Nguyen, H., Roe, D. R. & Simmerling, C. (2013). J. Chem. Theory Comput. 9, 2020-2034.
35. Perez, A., MacCallum, J. L., Brini, E., Simmerling, C. & Dill, K. A. (2015). J. Chem. Theory Comput. 11, 4770-4779.
36. Read, R. J. et al. (2011). Structure, 19, 1395-1412.
37. Rode, B. M., Schwenk, C. F., Hofer, T. S. & Randolf, B. R. (2005). Coord. Chem. Rev. 249, 2993-3006.
38. Stein, N. (2008). J. Appl. Cryst. 41, 641-643.
39. Stewart, D. E., Sarkar, A. & Wampler, J. E. (1990). J. Mol. Biol. 214, 253-260.
40. Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N.W., Zwart, P. H., Hung, L.-W., Read, R. J. & Adams, P. D. (2008). Acta Cryst. D64, 61-69.
41. Touw, W. G., Joosten, R. P. & Vriend, G. (2015). Acta Cryst. D71, 1604-1614.
42. Touw, W. G., van Beusekom, B., Evers, J. M. G., Vriend, G. & Joosten, R. P. (2016). Acta Cryst. D72, 1110-1118.
43. Trabuco, L. G., Villa, E., Mitra, K., Frank, J. & Schulten, K. (2008). Structure, 16, 673-683.
44. Wang, R. Y.-R., Song, Y., Barad, B. A., Cheng, Y., Fraser, J. S. & DiMaio, F. (2016). Elife, 5, e17219.
45. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
46. Wlodawer, A., Minor, W., Dauter, Z. & Jaskolski, M. (2013). FEBS J. 280, 5705-5736.