PrimeX References

1.

Read, R. J. Improved Fourier Coefficients for Maps Using Phases from Partial Structures with Errors. Acta Cryst. 1986, A42, 140–149.

2.

Bhat, T.N.; Cohen, G.H. OMIT MAP: An Electron Density Map Suitable for the Examination of Errors in a Macromolecular Model. J. Appl. Crystallog. 1984, 17, 244–248.

3.

Bhat, T.N. Calculation of an OMIT map. J. Appl. Crystallog. 1988, 21, 279–281.

4.

Vellieux, F. M. D.; Dijkstra, B. W. Computation of Bhat’s OMIT Maps with Different Coefficients. J. Appl. Crystallog. 1997, 30, 396–399.

5.

Pannu, N. S.; Read, R. J. Improved Structure Refinement through Maximum Likelihood. Acta Cryst. 1996, A52, 659–668.

6.

Brünger, A. T. A Memory-efficient Fourier Transformation algorithm for Crystallographic Refinement on Supercomnputers. Acta Cryst. 1989, A45, 42–50.

7.

Brünger, A. T.; Adams, P. D.; Clore, G. M.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J.-S.; Kuszewski, J.; Nilges, N.; Panu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Crystallograpy & NMR System (CNS): A New Software System for Macromolecular Structure Determination. Acta Cryst. 1998, D54, 905–921.

8.

Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Refinement of Macromolecular Structures by Maximum-Likelihood Method. Acta Cryst. 1997, D53, 240–255.

9.

Kaminski, G.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and Reparameterization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides. J. Phys. Chem. B 2001, 105, 6474–6487.

10.

Zhu, K.; Shirts, M. R.; Friesner, R. A. Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects. J. Chem. Theory Comput. 2007, 3, 2108–2119.

11.

Engh, R.A.; Huber, R. Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement. Acta Cryst. 1991, A47, 392–400.

12.

Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shaw, D. E.; Shelley, M.; Perry, J. K. Francis, P.; Shenkin, P. S. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy. J. Med. Chem. 2004, 47, 1739–1749.

13.

Banks, J. L.; Beard, H. S.; Cao, Y.; Cho, A. E.; Damm, W.; Farid, R.; Felts, A. K.; Halgren, T. A.; Mainz, D. T.; Maple, J. R.; Murphy, R.; Philipp, D. M.; Repasky, M. P.; Zhang, L. Y.; Berne, B. J.; Friesner, R. A.; Gallicchio, E.; Levy, R. M. Integrated Modeling Program. Applied Chemical Theory. (IMPACT). J. Comput. Chem. 2005, 26, 1752–80.

14.

Adams, P. D.; Pannu, N. S.; Read, A. T.; Brünger, A. T. Cross-validated Maximum-likelihood Enhances Crystallographic Simulated Annealing. Proc. Natl. Acad. Sci. USA 1997, 94, 5018–5023.

15.

Guncar G.; Klemencic, I.; Turk, B.; Turk, V.; Karaoglanovic-Carmona, A.; Juliano, L; Turk, D. Crystal structure of cathepsin X: a flip-flop of the ring of His23 allows carboxy-monopeptidase and carboxy-dipeptidase activity of the protease. Structure 2000, 8, 305.