Literature DB >> 32571067

Toward empirical force fields that match experimental observables.

Thorben Fröhlking1, Mattia Bernetti1, Nicola Calonaci1, Giovanni Bussi1.   

Abstract

Biomolecular force fields have been traditionally derived based on a mixture of reference quantum chemistry data and experimental information obtained on small fragments. However, the possibility to run extensive molecular dynamics simulations on larger systems achieving ergodic sampling is paving the way to directly using such simulations along with solution experiments obtained on macromolecular systems. Recently, a number of methods have been introduced to automatize this approach. Here, we review these methods, highlight their relationship with machine learning methods, and discuss the open challenges in the field.

Year:  2020        PMID: 32571067     DOI: 10.1063/5.0011346

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  7 in total

1.  Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models.

Authors:  Owen C Madin; Simon Boothroyd; Richard A Messerly; Josh Fass; John D Chodera; Michael R Shirts
Journal:  J Chem Inf Model       Date:  2022-02-07       Impact factor: 6.162

2.  Optimal Solution to the Torsional Coefficient Fitting Problem in Force Field Parametrization.

Authors:  Adrian Kania; Krzysztof Sarapata; Michał Gucwa; Anna Wójcik-Augustyn
Journal:  J Phys Chem A       Date:  2021-03-24       Impact factor: 2.781

3.  Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting.

Authors:  Stephan Thaler; Julija Zavadlav
Journal:  Nat Commun       Date:  2021-11-25       Impact factor: 14.919

4.  Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field.

Authors:  Thorben Fröhlking; Vojtěch Mlýnský; Michal Janeček; Petra Kührová; Miroslav Krepl; Pavel Banáš; Jiří Šponer; Giovanni Bussi
Journal:  J Chem Theory Comput       Date:  2022-06-14       Impact factor: 6.578

5.  Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine.

Authors:  Valerio Piomponi; Thorben Fröhlking; Mattia Bernetti; Giovanni Bussi
Journal:  ACS Cent Sci       Date:  2022-08-03       Impact factor: 18.728

Review 6.  Role and Perspective of Molecular Simulation-Based Investigation of RNA-Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding.

Authors:  Daria V Berdnikova; Paolo Carloni; Sybille Krauß; Giulia Rossetti
Journal:  Molecules       Date:  2021-06-03       Impact factor: 4.411

Review 7.  Hydroxylapatite and Related Minerals in Bone and Dental Tissues: Structural, Spectroscopic and Mechanical Properties from a Computational Perspective.

Authors:  Gianfranco Ulian; Daniele Moro; Giovanni Valdrè
Journal:  Biomolecules       Date:  2021-05-13
  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.