Journal of Chemical Information and Modeling
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Combining solvent thermodynamic profiles with functionality maps of the hsp90 binding site to predict the displacement of water molecules.
We employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if...
hERG me out.
A detailed analysis of the hERG content inside the ChEMBL database is performed. The correlation between the outcome from binding assays and functional assays is probed. On the basis of descriptor distributions, design paradigms with respect to structural and physicochemical properties of hERG activ...
Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark.
We introduce backbone flexibility into MedusaDock by implementing ensemble docking in a sequential manner for a set of distinct receptor backbone conformations. We generate corresponding backbone ensembles to capture backbone changes upon binding to different ligands, as observed experimentally. We...
Automated large-scale file preparation, docking, and scoring: evaluation of ITScore and STScore using the 2012 Community Structure-Activity ...
We use the recently released 2012 Community Structure-Activity Resource (CSAR) data set to evaluate two knowledge-based scoring functions, ITScore and STScore, and a simple force-field-based potential (VDWScore). The CSAR data set contains 757 compounds, most with known affinities, and 57 crystal st...
Structural properties of non-traditional drug targets present new challenges for virtual screening.
We systematically compare existing examples of inhibitors of protein-protein interactions to inhibitors of traditional drug targets. While both sets of inhibitors bind with similar potency, we find that the inhibitors of protein-protein interactions typically bury a smaller fraction of their surface...
Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding.
Our results may be particularly relevant in the design of novel drugs, which may be useful therapeutic treatments of cancers such as those of the breast and prostate....
Evaluation and optimization of virtual screening workflows with DEKOIS 2.0--a public library of challenging docking benchmark sets.
We aim to further extend and complement the collection of publicly available decoy sets. Based on BindingDB bioactivity data, we provide 81 new and structurally diverse benchmark sets for a wide variety of different target classes. To ensure a meaningful selection of ligands, we address several issu...
Building a Knowledge-Based Statistical Potential by Capturing High-Order Inter-residue Interactions and its Applications in Protein Secondar...
We report a context-based secondary structure potential (CSSP) for assessing the quality of predicted protein secondary structures generated by various prediction servers. CSSP is a sequence-position-specific knowledge-based potential generated based on the potentials of mean force approach, where h...
Elucidation of allosteric inhibition mechanism of 2-Cys human peroxiredoxin by molecular modeling.
We used molecular dynamics (MD) simulations and protein docking to elucidate the mechanism of allosteric inhibition of the human form of peroxiredoxin (Prx), 2-Cys proliferation associated gene (PAG). Beginning by using the rat form of Prx, 2-Cys heme-binding protein as a template, we used homology...
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges.
Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biological systems. In these simulations, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matchi...