System and method for molecular modeling utilizing a sensitivity factor

• US 5,612,894 A
• Filed: 02/08/1995
• Issued: 03/18/1997
• Est. Priority Date: 02/08/1995
• Status: Expired due to Fees

• Current Assignee: David H. Wertz
• Original Assignee: David H. Wertz
• Inventors: Wertz, David H.
• Primary Examiner(s): Voeltz, Emanuel T.
• Assistant Examiner(s): CHOI, KYLE JAEHUN
• Application Number:
  US08/390,600
• Time in Patent Office: 769 Days
• Field of Search: 364/496-499, 364/578, 364/527, 364/524
• US Class Current: 702/27
• CPC Class Codes: C07K 1/00 General methods for the preparation of peptides , i.e. processes for the organic chemical preparation of peptides or proteins of any length
• CPC Class Codes: G16C 10/00 Computational theoretical chemistry, i.e. ICT specially adapted for theoretical aspects of quantum chemistry, molecular mechanics, molecular dynamics or the like

Abstract

A computerized molecular modeling system is provided which graphically displays at least an initial and most likely structure of a molecule utilizing energy minimization and/or molecule dynamics techniques. The system utilizes a sensitivity factor to determine how often the less sensitive interactions, especially non-bonded interaction in a molecule should be recalculated during an energy minimization or molecular dynamics procedure. The sensitivity factor is based on each interaction'"'"'s sensitivity to changes in the positions of the atoms that comprise it.

Claims

1. A method for generating an image of a likely structure of a molecule, comprising the steps of:

(a) accepting as input into a computer an initial structure of the molecule, the initial structure of the molecule including a set of atom coordinates for the molecule;

(b) generating a set of interactions for each atom, each interaction corresponding to a force between its respective atom and one or more other atoms in the molecule;

(c) determining, from the initial structure of the molecule, a set of qualifying interactions and a set of non-qualifying interactions, the total set of interactions being a super-set of the set of qualifying interactions and the set of non-qualifying interactions;

(d) calculating a sensitivity factor for each interaction of the set of qualifying interactions based upon a sensitivity of the initial force of each interaction of the set of qualifying interactions with respect to changes in the position of the atoms which correspond to said each interaction, each sensitivity factor indicating a recalculation frequency for a respective interaction of the set of qualifying interactions;

(f) performing one of an energy minimization procedure and a molecular dynamics procedure, the step of performing including;

1) calculating a new force for each interaction of the set of interactions for an n-1^th structure of the molecule, the step of calculating further including the steps of;

(a) fully calculating a new force for each interaction of the set of non-qualifying interactions;

(b) fully calculating a new force for an interaction of the set qualifying interactions if the respective recalculation frequency for said interaction indicates that a previously calculated force is invalid;

(c) using a previously calculated force as the new force for an interaction of the set of qualifying interactions if the recalculation frequency for said interaction indicates that the previously calculated force is valid;

2) calculating a new total force for each atom by summing the new forces from all the interactions corresponding to said each atom;

3)using the new total forces for the n-1^th structure of the molecule to calculate an n^th structure of the molecule;

4) repeating step (f)(1-2) for n=1 through X interactions to generate X possible structures of the molecule,

(g) generating the image of the likely structure of the molecule, or a representative structure, or a sequence of structures based upon one or more of the X possible structures of the molecule.

2. A method for generating an image of a likely structure of a molecule, comprising the steps of:

(a) accepting as input into a computer an initial structure of the molecule, the initial structure of the molecule including a set of atom coordinates for the molecule;

(b) generating a set of interactions for each atom, each interaction corresponding to a force between its respective atom and one or more other atoms in the molecule;

(c) determining, from the initial structure of the molecule, a set of qualifying interactions and a set of non-qualifying interactions, the total set of interactions being a super-set of the set of qualifying interactions and the set of non-qualifying interactions;

(d) calculating a sensitivity factor for each interaction of the set of qualifying interactions based upon a sensitivity of the initial force of each interaction of the set of qualifying interactions with respect to changes in the position of the atoms which correspond to said each interaction, each sensitivity factor indicating a recalculation frequency for a respective interaction of the set of qualifying interactions;

(f) performing one of an energy minimization procedure and a molecular dynamics procedure, the step of performing including;

1) calculating a new force for each interaction of the set of interactions for an n-1^th structure of the molecule, the step of calculating further including the steps of;

(a) fully calculating a new force for each interaction of the set of non-qualifying interactions;

(b) fully calculating a new force for an interaction of the set qualifying interactions if the respective recalculation frequency for said interaction indicates that a previously calculated force is invalid;

(c) using an approximation for the new force for an interaction of the set of qualifying interactions if the recalculation frequency for said interaction indicates that the approximation invalid, said approximation being one of a previously calculated force, and a force calculated using a rapidly calculated equation;

2) calculating a new total force for each atom by summing the new forces from all the interactions corresponding to said each atom;

3) using the new total forces for the n-1^th structure of the molecule to calculate an n^th structure of the molecule;

4) repeating step (f)(1-2) for n=1 through X interactions to generate X possible structures of the molecule,

(g) generating the image of the likely structure of the molecule, or a representative structure, or a sequence of structures based upon one or more of the X possible structures of the molecule.

3. The method according to claim 2 wherein the sensitivity factor is defined as

4. The method according to claim 2 wherein each qualifying interaction is a non-bonded interaction for which the sensitivity factor is defined as

5. The method according to claim 2 wherein the sensitivity factor is defined as

6. The method according to claim 2 where in the sensitivity factor is defined as

7. The method according to claim 2 wherein the qualified interaction is a non-bonded interaction for which the sensitivity factor is defined as

8. The method according to claim 2 wherein the qualified interaction is a non-bonded interaction for which the sensitivity factor is defined as