11 papers · ranked by Valyu relevance
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Pharmacophores are widely used to describe protein-ligand interactions, and the Grids of Pharmacophore Interaction Fields (GRAIL) method extends this concept by representing binding pockets as interpretable sets of interaction type-specific pharmacophoric maps. In this work, we propose a hybrid framework for binding…
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Synthetic accessibility is a key issue in the current compound generation. Unlike conventional approaches that assess synthetic accessibility after compound generation, the fragment-based method proposed in this study links the fragments in the reverse direction of the retrosynthesis analysis guaranteeing the synthetic…
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Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, have become a gold standard tool for estimating compound affinity changes. Here we present the results of a large-scale…
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The analysis of molecular dynamics (MD) simulations is a critical but fragmented process, often requiring researchers to chain together multiple software tools and write bespoke scripts for routine structural and dynamic analyses. This workflow complexity creates a significant barrier to efficiency, standardization…
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Fragment-based drug discovery (FBDD) is a widely used strategy in early-stage drug development, but accurately predicting the binding affinities of fragments and their elaborated analogs poses unique computational challenges. These difficulties arise from weak binding affinities, diverse chemical scaffolds, and limited…
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The rapid growth of worldwide computing power has transformed in silico chemistry into a discipline that is integrated into the daily work of many chemists. Nowadays, researchers find it increasingly straightforward to predict a wide range of molecular properties and chemi- cal processes at reasonable computational…
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With the rapid growth of chemical data and information, there is an increasing need for chemistry undergraduates to master Python tools for analyzing large chemical datasets and extracting key or feature information. Currently, more than 100,000 types of metal-organic frameworks (MOFs), as the material recently awarded…
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Computational methods for predictive modeling have been increasingly utilized in the early stages of drug discovery to supplement high-throughput screening. The advent of highly efficient and complex machine learning architectures necessitates new methods of collating the plethora of topological, geometrical, and…
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Current methods for determining the neurotoxic potential of (agro)chemicals are not comprehensive enough, as is suggested by the increased incidence of Parkinson’s disease (PD) amongst people exposed to certain pesticides. Mechanism-based in silico screening can address this shortcoming by predicting molecular…
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End-point binding free energy (BFE) methods, such as molecular mechanics Poisson–Boltzmann surface area (MMPBSA), are widely used to estimate protein–ligand binding affinity due to their favorable balance between accuracy and computational efficiency. Their reliability, however, is often limited by approximations in…
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Preclinical studies indicate that selective targeting of D4R may improve behavioral and cognitive outcomes in animal models relevant to cognitive disorders, like ADHD and Alzheimer’s disease, and substance use disorders (SUDs). In this study, we extend upon prior development of analogs of A-412997, a D4R-selective…