Binding Affinity Prediction for Protein-Ligand Complexes Based on ß Contacts and B Factor

ACS Publications
Publication Type:
Journal Article
Journal of Chemical Information and Modeling, 2013, 53 (11), pp. 3076 - 3085
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Accurate determination of proteinligand binding affinity is a fundamental problem in biochemistry useful for many applications including drug design and proteinligand docking. A number of scoring functions have been proposed for the prediction of proteinligand binding affinity. However, accurate prediction is still a challenging problem because poor performance is often seen in the evaluation under the leave-one-cluster-out cross-validation (LCOCV). We introduce a new scoring function named B2BScore to improve the prediction performance. B2BScore integrates two physicochemical properties for proteinligand binding affinity prediction. One is the property of ß contacts. A ß contact between two atoms requires no other atoms to interrupt the atomic contact and assumes that the two atoms should have enough direct contact area. The other is the property of B factor to capture the atomic mobility in the dynamic proteinligand binding process.
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