C - Chemistry – Metallurgy – 40 – B
Patent
C - Chemistry, Metallurgy
40
B
C40B 30/02 (2006.01) G01N 33/53 (2006.01) G06F 19/00 (2006.01)
Patent
CA 2614995
A new approach to identifying binding conformations of chemical fragments and biological molecules is presented, in which fragment poses are explored in a systematic fashion. In an embodiment, for each pose, a fast computation is performed of the fragment interaction with the biological molecule using interpolation on a grid. Once the energies of fragment poses are computed, thermodynamical quantities such as binding affinity, binding enthalpy, and binding entropy are computed by direct sum over fragment poses. Using the present invention, it is possible to navigate fragment configuration space to identify separate binding modes. The present invention can be used to scan an entire biological molecule to identify possible binding pockets, or it can be used for localized explorations limited to interesting areas of known binding pockets.
Nouveau procédé d'identification de conformations de liaison de fragments chimiques et de molécules biologiques consistant à explorer les poses de ces fragments de façon systématique. Dans un mode de réalisation, on effectue un calcul rapide pour chaque pose, de l'interaction du fragment et de la molécule biologique au moyen d'une interpolation sur une grille. Une fois qu'on a calculé les énergies des poses des fragments, on calcule par addition continue au-dessus des poses des fragments, leurs quantités thermodynamiques, telles que l'affinité, l'enthalpie ou l'entropie de liaison. L'invention permet de naviguer dans l'espace de configuration des fragments afin d'identifier des modes de liaison séparés. On peut la mettre en application afin d'analyser la totalité d'une molécule biologique, de manière à identifier d'éventuelles poches de liaison ou afin d'effectuer des explorations localisées limitées à des zones intéressante de poches de liaison connues.
Carnevali Paolo
Meshkat Siavash N.
Toth Gergely
Borden Ladner Gervais Llp
Locus Pharmaceuticals Inc.
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