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Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm
Improved the docking accuracy did not necessarily enhance the ability to estimate binding affinities using the docked structures, and statistical analysis shows that even lower‐accuracy grid‐based energy representations can be effectively used when followed with full force field minimization. Expand
Synthesis and activity of new aryl- and heteroaryl-substituted pyrazole inhibitors of the transforming growth factor-beta type I receptor kinase domain.
Pyrazole-based inhibitors of the transforming growth factor-beta type I receptor kinase domain (TbetaR-I) are described and a common binding mode at the active site has been established by successful cocrystallization and X-ray analysis of potent inhibitors with the TbetaR -I receptor Kinase domain. Expand
Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.
The results show that docking accuracy falls off dramatically if one uses an average or apo structure, and it is shown that the drop in docking accuracy mirrors the degree to which the protein moves upon ligand binding. Expand
Kinomics-structural biology and chemogenomics of kinase inhibitors and targets.
The first dendrogram of kinases based entirely on small molecule selectivity data is presented, and it is found that the selectivitydendrogram differs from sequence-based clustering mostly in the higher-level groupings of the smaller clusters, and remains very comparable for closely homologous targets. Expand
Characteristic physical properties and structural fragments of marketed oral drugs.
Oral drugs tend to be lighter and have fewer H-bond donors, acceptors, and rotatable bonds than drugs with other routes of administration, and it is demonstrated that the mean property values for oral drugs do not vary substantially with respect to launch date, suggesting that the range of acceptable oral properties is independent of synthetic complexity or targeted receptor. Expand
Kinomics: characterizing the therapeutically validated kinase space.
Analysis of the similarity between kinase targets with respect to sequence, selectivity and structure has revealed that kinases with > or =60% sequence identity are most likely to be inhibited by the same classes of compounds and have similar ATP-binding sites. Expand
Assessing search strategies for flexible docking
This work assesses the efficiency of molecular dynamics MD, Monte Ž, Carlo MC, and genetic algorithms GA for docking five representative ligand]receptor complexes and finds that MD provides structures that are, on average, lower in energy and closer to the crystallographic conformation. Expand
Dependence of molecular properties on proteomic family for marketed oral drugs.
An association of drugs with their proteomic family reveals that molecular properties of drugs targeting proteases, lipid and peptide G-protein-coupled receptors (GPCRs), and nuclear hormoneExpand
Molecular properties that influence oral drug-like behavior.
This review will demonstrate how trends in simple properties of the data can be used prospectively to compare and prioritize groups of compounds, chemical libraries and different chemical series with greater reliability than for predicting drug-likeness of single compounds. Expand
Assessing energy functions for flexible docking
A good docking algorithm requires an energy function that is selective, in that it clearly differentiates correctly docked structures from misdocked ones, and that is efficient, meaning that aExpand