Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
We present , a versatile software for the automatic iterative parametrization of bonded parameters in coarse-grained (CG) models, ideal in combination with popular CG force fields such as MARTINI. By coupling fuzzy self-tuning particle swarm optimization to Boltzmann inversion, performs accurate bottom-up parametrization of bonded terms in CG models composed of up to 200 pseudo atoms within 4-24 h on standard desktop machines, using default settings. The software benefits from a user-friendly interface and two different usage modes (default and advanced). We particularly expect to support and facilitate the development of new CG models for the study of complex molecular systems interesting for bio- and nanotechnology. Excellent performances are demonstrated using a benchmark of 9 molecules of diverse nature, structural complexity, and size. is available with all its dependencies the Python Package Index (PIP package: ). Demonstration data are available at: www.github.com/GMPavanLab/SwarmCG.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758974 | PMC |
| http://dx.doi.org/10.1021/acsomega.0c05469 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Statistical Molecular Interaction Fields: A Fast and Informative Tool for Characterizing RNA and Protein-Binding Pockets.
J Chem Theory Comput
September 2025
Laboratoire Biologie Functionnelle et Adaptative, Université Paris Cité, Inserm ERL U1133, 35 Rue Hélène Brion, Paris 75013, France.
Developing a physical understanding of the interactions between a macromolecular target and its ligands is a crucial step in structure-based drug design. Although many tools exist to characterize protein-binding pockets in silico, this is not yet the case for RNA, which has been recognized only recently as a suitable target for small ligands. Molecular Interaction Fields (MIFs) are useful tools to characterize the interactions of a given binding pocket.
View Article and Find Full Text PDFAccuracy of Analog and Digital Full-Arch Mandibular Impressions: In Vitro and In Vivo Evaluation.
Diagnostics (Basel)
August 2025
Department of Prosthodontics, Faculty of Medicine, University of Pécs, Tüzér Street 1., H-7625 Pécs, Hungary.
Accurate full-arch impressions are crucial for predictable prosthodontic outcomes. While intraoral scanners (IOSs) are increasingly adopted, evidence comparing their accuracy with conventional analog impressions across full mandibular arches-particularly under both laboratory and clinical conditions using an objective intraoral reference-is limited. Our study aims to evaluate the in vitro and in vivo accuracy of digital impressions compared to conventional methods in full-arch scans using an intraoral reference tool.
View Article and Find Full Text PDFStatic and Vibration Analysis of Imperfect Thermoelastic Laminated Plates on a Winkler Foundation.
Materials (Basel)
July 2025
Langfang Sunshine Construction Engineering Quality Testing Co., Ltd., Langfang 065099, China.
This study introduces an analytical framework that integrates the state-space method with generalized thermoelasticity theory to obtain exact solutions for the static and dynamic behaviors of laminated plates featuring imperfect interfaces and resting on a Winkler foundation. The model comprehensively accounts for the foundation-structure interaction, interfacial imperfection, and the coupling between the thermal and mechanical fields. A parametric analysis explores the impact of the dimensionless foundation coefficient, interface flexibility coefficient, and thermal conductivity on the static and dynamic behaviors of the laminated plates.
View Article and Find Full Text PDFApplication of the novel BMEP monomer in experimental self-adhesive dental composite physicochemical and mechanical properties.
Odontology
August 2025
Department of Dental Biomaterials, School of Dentistry, Shahid Beheshti University of Medical Sciences, Velenjak Street, Tehran, Iran.
Adhesive dentistry has revolutionized with the proposal of self-adhesive composites (SACs), which aim to simplify restorative procedures by omitting the need for separate dental bonding agents' applications. Even though the limitations of these composites, including their questionable bond strength and long-term durability, remain our issues. Therefore, this in vitro study suggests a novel BMEP monomer designed to enhance the dental composite's physicochemical and mechanical properties.
View Article and Find Full Text PDFStatic strengths of circular hollow section stub column strengthened with carbon fiber reinforced polymer.
PLoS One
August 2025
Department of Mechanical and Information Engineering, Sichuan College of Architectural Technology, Deyang, China.
In previous studies, the strengthening effectiveness and feasibility of carbon fiber reinforced polymer (CFRP) were mainly evaluated through experimental research or numerical analysis. Although these methods can accurately provide estimates, both experimental and numerical assessment processes are costly in terms of time and cost. There is a need for reliable calculation formulae that can predict the static strengths of circular hollow section (CHS) stub columns in a more convenient and cost-saving manner.
View Article and Find Full Text PDF