J Chem Inf Model - Development of the knowledge-based and empirical combined scoring algorithm (KECSA) to score protein-ligand interactions.

Tópicos

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{ group(2977) signific(1463) compar(1072) }
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Resumo

We describe a novel knowledge-based protein-ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential. In this way, the LJ potential parameters were generated from protein-ligand complex structural data contained in the Protein Databank (PDB). Forty-nine (49) types of atomic pairwise interactions were derived using this method, which we call the knowledge-based and empirical combined scoring algorithm (KECSA). Two validation benchmarks were introduced to test the performance of KECSA. The first validation benchmark included two test sets that address the training set and enthalpy/entropy of KECSA. The second validation benchmark suite included two large-scale and five small-scale test sets, to compare the reproducibility of KECSA, with respect to two empirical score functions previously developed in our laboratory (LISA and LISA+), as well as to other well-known scoring methods. Validation results illustrate that KECSA shows improved performance in all test sets when compared with other scoring methods, especially in its ability to minimize the root mean square error (RMSE). LISA and LISA+ displayed similar performance using the correlation coefficient and Kendall t as the metric of quality for some of the small test sets. Further pathways for improvement are discussed for which would allow KECSA to be more sensitive to subtle changes in ligand structure.

Resumo Limpo

describ novel knowledgebas proteinligand score function employ new definit refer state allow us relat statist potenti lennardjon lj potenti way lj potenti paramet generat proteinligand complex structur data contain protein databank pdb fortynin type atom pairwis interact deriv use method call knowledgebas empir combin score algorithm kecsa two valid benchmark introduc test perform kecsa first valid benchmark includ two test set address train set enthalpyentropi kecsa second valid benchmark suit includ two largescal five smallscal test set compar reproduc kecsa respect two empir score function previous develop laboratori lisa lisa well wellknown score method valid result illustr kecsa show improv perform test set compar score method especi abil minim root mean squar error rmse lisa lisa display similar perform use correl coeffici kendal t metric qualiti small test set pathway improv discuss allow kecsa sensit subtl chang ligand structur

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