14 papers · ranked by Valyu relevance
Alejandro Martínez León, Lucas Andersen, Jochen S. Hub
User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA Authors: Alejandro Martínez León, Lucas Andersen, Jochen S. Hub We present BindFlow, a Python-based software for automated absolute binding free energy (ABFE) calculations at the free energy perturbation…
Yanli Wang, Frimpong Boadu, Jianlin Cheng, Lenore Cowen
MPBind was trained with true protein structures as input. To investigate how well it can predict binding sites from predicted protein structures, we randomly selected 20 protein chains for each of the five kinds of binding sites from Test2_data dataset (i.e. 100 protein chains in total) and applied AlphaFold 3 () to…
Mohammad Abdullah Aljasir, Sajjad Ahmad, Roberta Rocca, Alessia Bono + 1 more
Background/Objectives: GuaB, which is known as inosine 5′-phosphate dehydrogenase (IMPDH), is an enzymatic target involved in the de novo guanine biosynthetic pathway of the multidrug-resistant (MDR) Acinetobacter baumannii. GuaB has emerged as a potential therapeutic target to cope with increasing antibiotic…
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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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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…
Ainur Abukaev, Constantin Völter, Mikhail Romodin, Sebastian Schwartzkopff + 6 more
A new Python package, pygid, enables fast batch processing of X-ray scattering data, with a particular focus on grazing-incidence geometries.
Zeyi Zhang, Carlos Mora Perez, Patrick Kwon, Martin Head‐Gordon + 1 more
PARSEC.py is a Python-based real-space Kohn-Sham density functional theory (real-space KS-DFT) framework designed to provide a user- and developer-friendly platform for first-principles electronic-structure simulations. Discretization on real-space grids eliminates basis-set approximations, while enabling systematic…
Dylan Silke, Julie Iskander, Junqi Pan, Andrew P. Thompson + 3 more
Leveraging artificial intelligence and deep learning to generate proteins de novo (a.k.a. ‘synthetic proteins’) has unlocked new frontiers of protein design. Deep learning models trained on protein structures can generate novel protein designs that explore structural landscapes unseen by evolution. This approach…
Tomasz Chady, Zuzanna Karolina Filutowska, Zhiyong Lu
The eccLib library provides a high-performance solution for parsing GTF and FASTA files in Python, thereby significantly enhancing project performance. eccLib was built with the Python/C API in mind, allowing for performance closely matching that of native C parsers, which would not be feasible if implemented directly…
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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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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…