AmberTools

DA Case, HM Aktulga, K Belfon… - Journal of chemical …, 2023 - ACS Publications
AmberTools | Journal of Chemical Information and Modeling ACS ACS Publications C&EN CAS
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Biomolecular dynamics with machine-learned quantum-mechanical force fields trained on diverse chemical fragments

OT Unke, M Stöhr, S Ganscha, T Unterthiner… - Science …, 2024 - science.org
Molecular dynamics (MD) simulations allow insights into complex processes, but accurate
MD simulations require costly quantum-mechanical calculations. For larger systems, efficient …

[HTML][HTML] Unstructured linker regions play a role in the differential splicing activities of paralogous RNA binding proteins PTBP1 and PTBP2

A Truong, M Barton, U Tran, M Mellody… - Journal of Biological …, 2024 - ASBMB
RNA Binding Proteins regulate, in part, alternative pre-mRNA splicing and, in turn, gene
expression patterns. Polypyrimidine tract binding proteins PTBP1 and PTBP2 are …

Evaluating performance of the approximate 3D-RISM-KH molecular solvation theory for solvation free energies in alkanes and alkane-water partition coefficients

D Roy, A Kovalenko - Journal of Molecular Liquids, 2023 - Elsevier
The performance of the 3D-reference interaction site model (3D-RISM) with the Kovalenko-
Hirata (KH) closure is benchmarked for liquid alkanes. The liquids are modelled using the …

[HTML][HTML] Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction

L Casillas, VM Grigorian, T Luchko - Molecules, 2023 - mdpi.com
Hydration free energies of small molecules are commonly used as benchmarks for solvation
models. However, errors in predicting hydration free energies are partially due to the force …