Force fields, such as Amber's ff12SB, can be fairly accurate models of the physical forces in proteins and other biomolecules. When coupled with accurate solvation models, force fields are able to bring insight into the conformational preferences, transitions, pathways, and free energies for these biomolecules. When computational speed/cost matters, implicit solvent is often used but at the cost of accuracy. We present an empirical grid-like correction term, in the spirit of cMAPs, to the combination of the ff12SB protein force field and the GBneck2 implicit-solvent model. Ff12SB-cMAP is parametrized on experimental helicity data. We provide validation on a set of peptides and proteins. Ff12SB-cMAP successfully improves the secondary structure biases observed in ff12SB + Gbneck2. Ff12SB-cMAP can be downloaded ( https://github.com/laufercenter/Amap.git ) and used within the Amber package. It can improve the agreement of force fields + implicit solvent with experiments.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813323 | PMC |
| http://dx.doi.org/10.1021/acs.jctc.5b00662 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Generative Artificial Intelligence in Anatomic Pathology.
Arch Pathol Lab Med
January 2025
the Department of Pathology, The Ohio State University, Columbus (Parwani).
Context.—: Generative artificial intelligence (AI) has emerged as a transformative force in various fields, including anatomic pathology, where it offers the potential to significantly enhance diagnostic accuracy, workflow efficiency, and research capabilities.
Objective.
Motor decision-making under uncertainty and time pressure.
J Neurophysiol
February 2025
Centre for Sensorimotor Performance, School of Human Movement and Nutrition SciencesThe University of QueenslandBrisbaneQueenslandAustralia.
Purposeful movement often requires selection of a particular action from a range of alternatives, but how does the brain represent potential actions so that they can be compared for selection, and how are motor commands generated if movement is initiated before the final goal is identified? According to one hypothesis, the brain averages partially prepared motor plans to generate movement when there is goal uncertainty. This is consistent with the idea that motor decision-making unfolds through competition between internal representations of alternative actions. An alternative hypothesis holds that only one movement, which is optimized for task performance, is prepared for execution at any time.
View Article and Find Full Text PDFComparison Between Molecular Dynamics Potentials for Simulation of Graphene-Based Nanomaterials for Biomedical Applications.
Drug Dev Ind Pharm
January 2025
Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Jl. Raya Bandung Sumedang KM 21, Sumedang 45363, Indonesia.
Objective: This article provides a substantial review of recent research and comparison on molecular dynamics potentials to determine which are most suitable for simulating the phenomena in graphene-based nanomaterials (GBNs).
Significance: GBNs gain significant attention due to their remarkable properties and potential applications, notably in nanomedicine. However, the physical and chemical characteristics toward macromolecules that justify their nanomedical applications are not yet fully understood.
In Situ Mechanics of the Cytoskeleton.
Cytoskeleton (Hoboken)
January 2025
Department of Science, Yokohama City University, Yokohama, Japan.
Not only for man-made architecture but also for living cells, the relationship between force and structure is a fundamental properties that governs their mechanical behaviors. However, our knowledge of the mechanical properties of intracellular structures is very limited because of the lack of direct measurement methods. We established high-force intracellular magnetic tweezers that can generate calibrated forces up to 10 nN, enabling direct force measurements of the cytoskeleton.
View Article and Find Full Text PDFMethane Bubbled Through Seawater Can be Converted to Methanol With High Efficiency.
Adv Sci (Weinh)
January 2025
Department of Chemistry, Stanford University, 380 Roth Way, Stanford, CA, 94305, USA.
Partial oxidation of methane (POM) is achieved by forming air-methane microbubbles in saltwater to which an alternating electric field is applied using a copper oxide foam electrode. The solubility of methane is increased by putting it in contact with water containing dissolved KCl or NaCl (3%). Being fully dispersed as microbubbles (20-40 µm in diameter), methane reacts more fully with hydroxyl radicals (OH·) at the gas-water interface.
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!