Methods and systems for molecular inhibition
Methods and systems are described which identify the structure of a biochemical or pathogenic molecule as well as at least one interacting molecule structure. These structures may be predicted to form at least one complex. In some embodiments, the stability and toxicity of at least one molecule structure and/or complex may be predicted.
1 . A computer-implemented method comprising:
predicting a structural model of a first complex consisting essentially of a biochemical molecule structure and a first interacting molecule structure;
in response to the predicted structural model of the first complex, selecting a second interacting molecule structure predicted to associate with the first complex;
predicting a structural model of a second complex, consisting essentially of the first complex and the second interacting molecule structure; and
in response to the predicted structural model of the second complex, selecting a third interacting molecule structure predicted to associate with the second complex.
2 . (canceled)
3 . The method as in claim 1 , further comprising:
predicting the stability of the interaction between the molecule structures forming the first complex; and
selecting the second interacting molecule structure in response to the predicted stability of the interaction between the molecule structures forming the first complex.
4 . (canceled)
5 . The method as in claim 1 , further comprising:
predicting the stability of the interaction between the molecule structures forming the second complex; and
selecting the third interacting molecule structure in response to the predicted stability of the interaction between the molecule structures forming the second complex.
6 . (canceled)
7 . The method as in claim 1 further comprising:
selecting a series of N additional interacting molecule structures wherein each interacting molecule structure is predicted to associate with the N-1 complex; and
predicting a structural model of each of N complexes, which consist essentially of the N-1 complex and the N interacting molecule structures.
8 . (canceled)
9 . The method as in claim 7 , wherein the selection of each additional interacting molecule structure is in response to the predicted stability of the interaction between the molecule structures forming the most recently predicted complex.
10 . The method as in claim 1 wherein the structural model of the second complex predicts that the second interacting molecule structure associates with both the biochemical molecule structure and the first interacting molecule structure.
11 . (canceled)
12 - 21 . (canceled)
22 . The method as in claim 1 wherein predicting a structural model of the first complex includes a 3-dimensional structure prediction.
23 - 25 . (canceled)
26 . The method as in claim 1 wherein predicting a structural model of a first complex includes accessing information regarding crystal structure.
27 . (canceled)
28 - 32 . (canceled)
33 . (canceled)
34 . The method as in claim 1 wherein predicting a structural model of a second complex includes a 3-dimensional structure prediction.
35 - 37 . (canceled)
38 . The method as in claim 1 wherein predicting a structural model of a second complex includes accessing information regarding crystal structure.
39 . (canceled)
40 - 46 . (canceled)
47 . The method as in claim 1 wherein the biochemical molecule structure corresponds to a molecule that is causally associated with a disease state in a human.
48 . (canceled)
49 . The method as in claim 1 wherein the biochemical molecule structure corresponds to a molecule that is casually associated with a disease state in a non-domestic animal.
50 . The method as in claim 1 wherein the biochemical molecule structure corresponds to a molecule that is an enzyme.
51 - 52 . (canceled)
53 . (canceled)
54 . (canceled)
55 - 56 . (canceled)
57 . A computer-implemented method comprising:
A. identifying an interacting molecule structure that is predicted to form a primary complex with a pathogenic molecule structure;
B. predicting the structure of the primary complex formed by the pathogenic molecule structure and the interacting molecule structure;
C. identifying a secondary interacting molecule structure that is predicted to form a secondary complex in association with the primary complex;
D. predicting a structure of the secondary complex; and
E. identifying at least one additional interacting molecule structure predicted to form a tertiary complex in association with the secondary complex.
58 . The method as in claim 57 wherein formation of the primary complex is predicted to inhibit activity of the pathogenic molecule corresponding to the pathogenic molecule structure.
59 . The method as in claim 57 wherein the pathogenic molecule corresponding to the pathogenic molecule structure is predicted to have less activity when it is a part of the primary complex than it has when it is not part of the primary complex.
60 . The method as in claim 57 wherein the pathogenic molecule corresponding to the pathogenic molecule structure is predicted to have less activity when it is a part of the secondary complex than it has when it is a part of the primary complex only.
61 . (canceled)
62 . The method as in claim 57 wherein the conformation of the pathogenic molecule structure is predicted to be altered by formation of the primary complex.
63 . (canceled)
64 . The method as in claim 57 wherein the conformation of the pathogenic molecule structure is predicted to be altered by formation of the tertiary complex.
65 - 69 . (canceled)
70 . The method as in claim 57 wherein the pathogenic molecule corresponding to the pathogenic molecule structure is casually associated with a disease state in a human.
71 . (canceled)
72 . The method as in claim 57 wherein the pathogenic molecule corresponding to the pathogenic molecule structure is an enzyme.
73 - 97 . (canceled)
98 . A computer-implemented method comprising:
predicting a structural model of a first complex consisting essentially of a biochemical molecule structure and a first interacting molecule structure;
in response to the predicted structural model of the first complex, selecting a second interacting molecule structure predicted to associate with the first complex;
predicting a structural model of a second complex, consisting essentially of the first complex and the second interacting molecule structure;
in response to the predicted structural model of the second complex, selecting a third interacting molecule structure predicted to associate with the second complex; and
predicting a structural model of a third complex, consisting essentially of the second complex and the third interacting molecule structure.
99 . The method as in claim 98 wherein the structural model of the third complex predicts that the third interacting molecule structure directly associates with the biochemical molecule structure, the first interacting molecule structure and the second interacting molecule structure simultaneously.
100 . (canceled)
101 . The method as in claim 98 wherein the structural model of the third complex predicts that the third interacting molecule structure does not directly associate with the second interacting molecule structure.
102 . The method as in claim 98 , further comprising:
predicting activity of molecules corresponding to molecular structures in the third complex.
103 . (canceled)