CHARMM at 45: Enhancements in accessibility, functionality, and speed
W Hwang, SL Austin, A Blondel… - The Journal of …, 2024 - ACS Publications
Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …
computational biochemistry and biophysics. Commensurate with the developments in …
Constant ph molecular dynamics simulations: Current status and recent applications
Many important protein functions are carried out through proton-coupled conformational
dynamics. Thus, the ability to accurately model protonation states dynamically has wide …
dynamics. Thus, the ability to accurately model protonation states dynamically has wide …
GPU-accelerated all-atom particle-mesh Ewald continuous constant pH molecular dynamics in Amber
JA Harris, R Liu, V Martins de Oliveira… - Journal of chemical …, 2022 - ACS Publications
Constant pH molecular dynamics (MD) simulations sample protonation states on the fly
according to the conformational environment and user specified pH conditions; however, the …
according to the conformational environment and user specified pH conditions; however, the …
Assessing lysine and cysteine reactivities for designing targeted covalent kinase inhibitors
Targeted covalent inhibitor design is gaining increasing interest and acceptance. A typical
covalent kinase inhibitor design targets a reactive cysteine; however, this strategy is limited …
covalent kinase inhibitor design targets a reactive cysteine; however, this strategy is limited …
Binding of inhibitors to BACE1 affected by pH-dependent protonation: An exploration from multiple replica Gaussian accelerated molecular dynamics and MM-GBSA …
J Chen, S Zhang, W Wang, H Sun… - ACS Chemical …, 2021 - ACS Publications
To date, inhibiting the activity of β-amyloid cleaving enzyme 1 (BACE1) has been
considered an efficient approach for treating Alzheimer's disease (AD). In the current work …
considered an efficient approach for treating Alzheimer's disease (AD). In the current work …
Dynamic protonation dramatically affects the membrane permeability of drug-like molecules
Permeability (P m) across biological membranes is of fundamental importance and a key
factor in drug absorption, distribution, and development. Although the majority of drugs will …
factor in drug absorption, distribution, and development. Although the majority of drugs will …
GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations
RC Harris, J Shen - Journal of chemical information and modeling, 2019 - ACS Publications
We present a GPU implementation of the continuous constant pH molecular dynamics
(CpHMD) based on the most recent generalized Born implicit-solvent model in the pmemd …
(CpHMD) based on the most recent generalized Born implicit-solvent model in the pmemd …
Reactivities of the front pocket N-terminal cap cysteines in human kinases
The front pocket (FP) N-terminal cap (Ncap) cysteine is the most popular site of covalent
modification in kinases. A long-standing hypothesis associates the Ncap position with …
modification in kinases. A long-standing hypothesis associates the Ncap position with …
[HTML][HTML] A guide to the continuous constant pH molecular dynamics methods in Amber and CHARMM [Article v1. 0]
Like temperature and pressure, solution pH is an important environmental variable in
biomolecular simulations. Virtually all proteins depend on pH to maintain their structure and …
biomolecular simulations. Virtually all proteins depend on pH to maintain their structure and …
Protein pKa Prediction with Machine Learning
Z Cai, F Luo, Y Wang, E Li, Y Huang - ACS omega, 2021 - ACS Publications
Protein p K a prediction is essential for the investigation of the pH-associated relationship
between protein structure and function. In this work, we introduce a deep learning-based …
between protein structure and function. In this work, we introduce a deep learning-based …