From the 1 of 14 linked papers with an AI index.
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Improved Treatment of 1-4 interactions in Force Fields for Molecular Dynamics Simulations
Aalim S. Abdullah, Yingze Wang, Maximilian F. S. J. Menger +2
Traditional force fields commonly use a combination of bonded torsional terms and empirically scaled non-bonded interactions to capture 1-4 energies and forces of atoms separated b…
SynLlama: Generating Synthesizable Molecules and Their Analogs with Large Language Models
Kunyang Sun, Dorian Bagni, Joseph M. Cavanagh +6
Generative machine learning models for exploring chemical space have shown immense promise, but many molecules they generate are too difficult to synthesize, making them impractica…
Determining the Role of Electrostatics in the Making and Breaking of the Caprin1-ATP Nanocondensate
Maria Tsanai, Teresa Head-Gordon
We employ a multiscale computational approach to investigate the condensation process of the C-terminal low-complexity region of the Caprin1 protein as a function of increasing ATP…
Deep Learning of Proteins with Local and Global Regions of Disorder
Oufan Zhang, Zi Hao Liu, Julie D Forman-Kay +1
Although machine learning has transformed protein structure prediction of folded protein ground states with remarkable accuracy, intrinsically disordered proteins and regions (IDPs…
A Workflow to Create a High-Quality Protein-Ligand Binding Dataset for Training, Validation, and Prediction Tasks
Yingze Wang, Kunyang Sun, Jie Li +4
Development of scoring functions (SFs) used to predict protein-ligand binding energies requires high-quality 3D structures and binding assay data for training and testing their par…