GeomBD3 is a robust Brownian dynamics simulation package designed to easily handle natural or engineered systems in diverse environments and arrangements. The software package described herein allows users to design, execute, and analyze BD simulations. The simulations use all-atom, rigid molecular models that diffuse according to overdamped Langevin dynamics and interact through electrostatic, Lennard-Jones, and ligand desolvation potentials. The program automatically calculates molecular association rates, surface residence times, and association statistics for any number of user-defined association criteria. Users can also extract molecular association pathways, diffusion coefficients, intermolecular interaction energies, intermolecular contact probability maps, and more using the provided supplementary analysis scripts. We detail the use of the package from start to finish and apply it to a protein-ligand system and a large nucleic acid biosensor. GeomBD3 provides a versatile tool for researchers from various disciplines that can aid in rational design of engineered systems or play an explanatory role as a complement to experiments. GeomBD version 3 is available on our website at http://chemcha-gpu0.ucr.edu/geombd3/ and KBbox at https://kbbox.h-its.org/toolbox/methods/molecular-simulation/geombd/.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9308565 | PMC |
| http://dx.doi.org/10.1021/acs.jcim.1c01387 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Urgency Prediction for Medical Laboratory Tests Through Optimal Sparse Decision Tree: Case Study With Echocardiograms.
JMIR AI
January 2025
Department of Information Systems and Business Analytics, Iowa State University, Ames, IA, United States.
Background: In the contemporary realm of health care, laboratory tests stand as cornerstone components, driving the advancement of precision medicine. These tests offer intricate insights into a variety of medical conditions, thereby facilitating diagnosis, prognosis, and treatments. However, the accessibility of certain tests is hindered by factors such as high costs, a shortage of specialized personnel, or geographic disparities, posing obstacles to achieving equitable health care.
View Article and Find Full Text PDFDiagnostic Decision-Making Variability Between Novice and Expert Optometrists for Glaucoma: Comparative Analysis to Inform AI System Design.
JMIR Med Inform
January 2025
Department of Systems Design Engineering, Faculty of Engineering, University of Waterloo, Waterloo, ON, Canada.
Background: While expert optometrists tend to rely on a deep understanding of the disease and intuitive pattern recognition, those with less experience may depend more on extensive data, comparisons, and external guidance. Understanding these variations is important for developing artificial intelligence (AI) systems that can effectively support optometrists with varying degrees of experience and minimize decision inconsistencies.
Objective: The main objective of this study is to identify and analyze the variations in diagnostic decision-making approaches between novice and expert optometrists.
How Do the Valency and Radii of Cations Affect the Rheological Properties of Aqueous Solutions of Zwitterionic and Anionic Surfactant Mixtures?
Langmuir
January 2025
Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, ul. Berdychowo 4, PL 60-965 Poznan, Poland.
Despite extensive research on the use of salts to enhance micellar growth, numerous questions remain regarding the impact of ionic exchange and molecular structure on charge neutralization. This study looks into how certain cations (Na, Ca, and Mg) affect the structure of a cocamidopropyl betaine CAPB and sodium dodecylbenzenesulfonate SDBS surfactant mixture, aiming toward applications in targeted delivery systems. The mixture consists of a zwitterionic surfactant, cocamidopropyl betaine (CAPB), and an anionic surfactant, sodium dodecylbenzenesulfonate (SDBS), combined in varying molar ratios at a total concentration of 200 mM.
View Article and Find Full Text PDFQuantum Analog of Landau-Lifshitz-Gilbert Dynamics.
Phys Rev Lett
December 2024
Uppsala University, Department of Physics and Astronomy, Box 516, SE-751 20 Uppsala, Sweden.
The Landau-Lifshitz-Gilbert (LLG) and Landau-Lifshitz (LL) equations play an essential role for describing the dynamics of magnetization in solids. While a quantum analog of the LL dynamics has been proposed in [Phys. Rev.
View Article and Find Full Text PDFDressed Majorana Fermion in a Hybrid Nanowire.
Phys Rev Lett
December 2024
Beijing Computational Science Research Center, Beijing 100193, China.
In hybrid systems where nanowires are proximity-coupled with superconductors, the low-energy theory fails to determine the topological phase with Majorana fermion (MF) when the magnetic field or proximity coupling is much stronger. To overcome this limitation, we propose a holistic approach that defines MF by considering both the motion of electrons in the nanowire and the quasiparticle excitations in the superconductor. This approach transcends the constraints of low-energy theory and offers broad applicability.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!