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Iodide Binding in Sodium-Coupled Cotransporters
10.1021/acs.jcim.7b00521 2017-12-04 Several apical iodide translocation pathways have been proposed for iodide efflux out of thyroid follicular cells, including a pathway mediated by the sodium-coupled monocarboxylate transporter 1 (SMCT1), which remains controversial. Herein, we evaluate struc... |
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Predicted Biological Activity of Purchasable Chemical Space
10.1021/acs.jcim.7b00316 2017-12-01 Whereas 400 million distinct compounds are now purchasable within the span of a few weeks, the biological activities of most are unknown. To facilitate access to new chemistry for biology, we have combined the Similarity Ensemble Approach (SEA) with the maxim... |
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Divergent Spatiotemporal Interaction of Angiotensin Receptor Blocking Drugs with Angiotensin Type1 Receptor
10.1021/acs.jcim.7b00424 2017-12-01 Crystal structures of the human angiotensin II type 1 receptor (AT1R) complex with the anti-hypertensive agent ZD7155 (PDB id: 4YAY) and the blood pressure medication Benicar (PDB id: 4ZUD) showed that binding poses of both antagonists are similar. This findi... |
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Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model
10.1021/acs.jcim.7b00510 2017-12-01 A protocol for predicting the hydrophobic length of membrane proteins using the heterogeneous dielectric generalized Born (HDGB) implicit membrane model is presented. The method involves optimal positioning in the membrane and identification of lipid-facing a... |
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Bioisostere Identification by Determining the Amino Acid Binding Preferences of Common Chemical Fragments
10.1021/acs.jcim.7b00092 2017-12-01 To assist in the structural optimization of hit/lead compounds during drug discovery, various computational approaches to identify potentially useful bioisosteric conversions have been reported. Here, the preference of chemical fragments to hydrogen bonds wit... |
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Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson–Boltzmann Surface Area (FMO+MM-PBSA) Approach
10.1021/acs.jcim.7b00110 2017-12-01 Significant activity changes due to small structural changes (i.e., activity cliffs) of serine/threonine kinase Pim1 inhibitors were studied theoretically using the fragment molecular orbital method with molecular mechanics Poisson–Boltzmann surface area (FMO... |
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Searching Online Chemical Data Repositories via the ChemAgora Portal
10.1021/acs.jcim.7b00086 2017-11-30 ChemAgora, a web application designed and developed in the context of the “Data Infrastructure for Chemical Safety Assessment” (diXa) project, provides search capabilities to chemical data from resources available online, enabling users to cross-reference the... |
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Task-Specific Scoring Functions for Predicting Ligand Binding Poses and Affinity and for Screening Enrichment
10.1021/acs.jcim.7b00309 2017-11-30 Molecular docking, scoring, and virtual screening play an increasingly important role in computer-aided drug discovery. Scoring functions (SFs) are typically employed to predict the binding conformation (docking task), binding affinity (scoring task), and bin... |
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Descriptor Data Bank (DDB): A Cloud Platform for Multi-Perspective Modeling of Protein-Ligand Interactions
10.1021/acs.jcim.7b00310 2017-11-29 Protein-ligand (PL) interactions play a key role in many life processes such as molecular recognition, molecular binding, signal transmission, and cell metabolism. Examples of interaction forces include hydrogen bonding, hydrophobic effects, steric clashes, e... |
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Parallel Tempering of Dark Matter from the Ebola Virus Proteome: Comparison of CHARMM36m and CHARMM22 Force Fields with Implicit Solvent
10.1021/acs.jcim.7b00517 2017-11-29 Intrinsically disordered proteins are characterized by their large manifold of thermally accessible conformations and their related statistical weights making them an interesting target of simulation studies. To assess the development of a computational frame... |