[Halgren-1999] | Halgren, T. A., MMFF VI. MMFF94s Option for Energy Minimization Studies., J. Comp. Chem. 20, 720- 729. (1999b). |
[Menendez-2003] | Menendéz-Velazquez, A., Garcià-Granda, S., A procedure towards the automatic solution of crystal structures by means of topological analysis of Fourier maps, J. Appl. Cryst. Vol 36, pp. 193-205, 2003 |
[Diller-1999] | Diller, D.J., Verlinde, C., A critical evaluation of several global optimization algorithms for the purpose of molecular docking. J. Comp. Chem, Vol. 20, 1740-1751, 1999 |
[Koch-1974] | Koch, M.H., Automatic interpretation of electron-density maps for organic structures., Acta Cryst A, Vol. 30, pp. 67-70, 1974 |
[Main-1978] | Main, P., Hull, S., The recognition of molecular fragments in E maps and electron density maps, Acta Cryst A, Vol. 34, pp. 353-361, 1978 |
[Cascarano-1991] | Cascarano, G., Giacovazzo, C., Camalli, M., Spagna, R., Watkin, D., Automatic solution and refinement of crystal structures by means of the package UNIQUE, Acta. Cryst. A, Vol. 47, pp. 373-381, 1991 |
[Altomare-2002] | Altomare, A., Giacovazzo, C., Ianigro, M., Moliterni, A., Rizzi, R., Peak labelling in electron density maps from powder data: the use of crystal chemical information, J. Appl. Cryst., Vol. 35, pp. 21-27, 2002 |
[Zwart-2004] | Zwart, P., Langer G., Lamzin V., Modelling bound ligands in protein crystal structures, Acta Cryst D, Vol 60, pp. 2230-2239, 2004 |
[Oldfield-2001] | Oldfield, T., Creating structure features by data mining the PDB to use as molecular-replacement models, Acta Cryst. D, Vol 57, pp. 696-705, 2001 |
[Perola-2004] | Perola E., Charifson P.S., Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding, J. Med. Chem., Vol. 47, pp. 2499-510, 2004 |
[Wlodek-2005] | Wlodek, S., Skillman A.G., Nicholls A., Automated ligand placement and refinement with a combined force field and shape potential, Acta Cryst. D, 2005. |
[Vagin-2004] | Vagin A.A., Steiner R.A., Lebedev A.A., Potterton L., McNicholas S., Long F. and Murshudov G.N., REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use, Acta Cryst D., Vol. 60, pp. 2184-2195, 2004 |
[Murshudov-1997] | Murshudov G.N., Vagin A.A., Dodson E.J., Refinement of Macromolecularstructures by Maximum likelihood method. Acta Cryst. D Vol. 53, pp. 240-255, 1997 |
[Adams-2010] | P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. “PHENIX: a comprehensive Python-based system for macromolecular structure solution.” Acta Cryst., D66, 213-221 2010 |
[Brunger-1998] | Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.-S., Kuszewski J., Nilges M., Pannu N.S., Read R.J., Rice L.M.,Simonson T. and Warren G.L., CNS/CNX Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination Acta Cryst. (1998). D54, 905-921 |
[Eldridge-1997] | M.D. Eldridge, C.W. Murray, T.R. Auton, G.V. Paolini, R.P. Mee, “Empirical scoring functions. I: The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes,” J. Comput.- Aided Mol. Des., 11, 1997, pp. 425-445 |
[Verkhivker-2000] | Verkhivker, GM, Bouzida, D, Gehlhaar, DK, Rejto, PA, Arthurs, S, Colson, AB, Freer, ST, Larson, V, Luty, BA, Marrone, T, and Rose, PW, “Deciphering common failures in molecular docking of ligand-protein complexes”, Journal of Computer-Aided Molecular Design, 14(2000), 731-751) |
[public-monomers] | http://pdb.rutgers.edu/public-component-erf.cif |
[EDS] | GJ Kleywegt, MR Harris, JY Zou, TC Taylor, A Wählby & TA Jones (2004), The Uppsala Electron-Density Server, Acta Cryst. D60, 2240-2249 |