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PrimeX and the Schrödinger computational chemistry suite of programs
International Tables for Crystallography (2012). Vol. F, ch. 18.10, pp. 534-538 [ doi:10.1107/97809553602060000864 ]
... Banks, J. L., Beard, H. S., Cao, Y., Cho, A. E., Damm, W., Farid, R., Felts, A. K., Halgren, T. A. ... P., Zhang, L. Y., Berne, B. J., Friesner, R. A., Gallicchio, E. & Levy, R. M. (2005). Integrated Modeling Program, Applied ...
Validation
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.6, pp. 537-538 [ doi:10.1107/97809553602060000864 ]
Validation 18.10.4.6. Validation PrimeX provides three main validation tools. `Protein reports' lists geometric variations from expected values in table form. This table can be sorted by residue or by the magnitude of the deviation, to highlight parts of the structure most in need of attention. A density fit table (Fig.18.10.4.2) lists ...
[more results from section 18.10.4 in volume F]
Automation of refinement tasks
International Tables for Crystallography (2012). Vol. F, Section 18.10.3.3, p. 536 [ doi:10.1107/97809553602060000864 ]
Automation of refinement tasks 18.10.3.3. Automation of refinement tasks As well as executing through the graphical interface, most PrimeX tasks can be run through command-line execution, so these tasks can be easily integrated into workflows. Future development will be focused on combining multiple tasks and diagnostic information into larger automated ...
[more results from section 18.10.3 in volume F]
Molecular mechanics
International Tables for Crystallography (2012). Vol. F, Section 18.10.2.3, p. 535 [ doi:10.1107/97809553602060000864 ]
Molecular mechanics 18.10.2.3. Molecular mechanics OPLS (Jorgensen et al., 1996; Kaminski et al., 2001) is a general-purpose force field for modelling proteins, nucleic acids and small molecules. This accurate description of atomic level interactions provides consistency across all Schrödinger molecular modelling packages, such as the core modelling functions of ...
[more results from section 18.10.2 in volume F]
Implementation path
International Tables for Crystallography (2012). Vol. F, Section 18.10.1.3, p. 534 [ doi:10.1107/97809553602060000864 ]
Implementation path 18.10.1.3. Implementation path In a field where most of the available software has been developed from academic sources, PrimeX is the only refinement program for biological crystallography that has been developed in a commercial environment. The advantage of commercial development includes high standards for consistency, professional software support and ...
[more results from section 18.10.1 in volume F]
Conclusion
International Tables for Crystallography (2012). Vol. F, Section 18.10.5, p. 538 [ doi:10.1107/97809553602060000864 ]
... Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235-242. Knight, J. L., Zhou, Z., Gallicchio, E., Himmel, D. M., Friesner, R. A., Arnold, E. & Levy, ...
International Tables for Crystallography (2012). Vol. F, ch. 18.10, pp. 534-538 [ doi:10.1107/97809553602060000864 ]
... Banks, J. L., Beard, H. S., Cao, Y., Cho, A. E., Damm, W., Farid, R., Felts, A. K., Halgren, T. A. ... P., Zhang, L. Y., Berne, B. J., Friesner, R. A., Gallicchio, E. & Levy, R. M. (2005). Integrated Modeling Program, Applied ...
Validation
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.6, pp. 537-538 [ doi:10.1107/97809553602060000864 ]
Validation 18.10.4.6. Validation PrimeX provides three main validation tools. `Protein reports' lists geometric variations from expected values in table form. This table can be sorted by residue or by the magnitude of the deviation, to highlight parts of the structure most in need of attention. A density fit table (Fig.18.10.4.2) lists ...
[more results from section 18.10.4 in volume F]
Automation of refinement tasks
International Tables for Crystallography (2012). Vol. F, Section 18.10.3.3, p. 536 [ doi:10.1107/97809553602060000864 ]
Automation of refinement tasks 18.10.3.3. Automation of refinement tasks As well as executing through the graphical interface, most PrimeX tasks can be run through command-line execution, so these tasks can be easily integrated into workflows. Future development will be focused on combining multiple tasks and diagnostic information into larger automated ...
[more results from section 18.10.3 in volume F]
Molecular mechanics
International Tables for Crystallography (2012). Vol. F, Section 18.10.2.3, p. 535 [ doi:10.1107/97809553602060000864 ]
Molecular mechanics 18.10.2.3. Molecular mechanics OPLS (Jorgensen et al., 1996; Kaminski et al., 2001) is a general-purpose force field for modelling proteins, nucleic acids and small molecules. This accurate description of atomic level interactions provides consistency across all Schrödinger molecular modelling packages, such as the core modelling functions of ...
[more results from section 18.10.2 in volume F]
Implementation path
International Tables for Crystallography (2012). Vol. F, Section 18.10.1.3, p. 534 [ doi:10.1107/97809553602060000864 ]
Implementation path 18.10.1.3. Implementation path In a field where most of the available software has been developed from academic sources, PrimeX is the only refinement program for biological crystallography that has been developed in a commercial environment. The advantage of commercial development includes high standards for consistency, professional software support and ...
[more results from section 18.10.1 in volume F]
Conclusion
International Tables for Crystallography (2012). Vol. F, Section 18.10.5, p. 538 [ doi:10.1107/97809553602060000864 ]
... Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235-242. Knight, J. L., Zhou, Z., Gallicchio, E., Himmel, D. M., Friesner, R. A., Arnold, E. & Levy, ...
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