Coarse-grained protein models and their applications

S Kmiecik, D Gront, M Kolinski, L Wieteska… - Chemical …, 2016 - ACS Publications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

[HTML][HTML] Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

S Piana, JL Klepeis, DE Shaw - Current opinion in structural biology, 2014 - Elsevier
Highlights•The accuracy of physical models used in protein-folding simulations is
assessed.•This assessment is based on data from very long molecular dynamics …

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

RB Best, X Zhu, J Shim, PEM Lopes… - Journal of chemical …, 2012 - ACS Publications
While the quality of the current CHARMM22/CMAP additive force field for proteins has been
demonstrated in a large number of applications, limitations in the model with respect to the …

A multi-analytical approach to peer-to-peer mobile payment acceptance prediction

Z Kalinic, V Marinkovic, S Molinillo… - Journal of Retailing and …, 2019 - Elsevier
This research is a pioneering study into peer-to-peer mobile payment (P2PM-pay) systems'
adoption. It proposes a behavioral model of the use of P2PM-pay systems and identifies the …

Improved side‐chain torsion potentials for the Amber ff99SB protein force field

K Lindorff‐Larsen, S Piana, K Palmo… - Proteins: Structure …, 2010 - Wiley Online Library
Recent advances in hardware and software have enabled increasingly long molecular
dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of …

freud: A software suite for high throughput analysis of particle simulation data

V Ramasubramani, BD Dice, ES Harper… - Computer Physics …, 2020 - Elsevier
The freud Python package is a library for analyzing simulation data. Written with modern
simulation and data analysis workflows in mind, freud provides a Python interface to fast …

Atomic-level characterization of the structural dynamics of proteins

DE Shaw, P Maragakis, K Lindorff-Larsen, S Piana… - Science, 2010 - science.org
Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic
level of detail, but they have been limited to time scales shorter than those of many …

Biomolecular simulation: a computational microscope for molecular biology

RO Dror, RM Dirks, JP Grossman, H Xu… - Annual review of …, 2012 - annualreviews.org
Molecular dynamics simulations capture the behavior of biological macromolecules in full
atomic detail, but their computational demands, combined with the challenge of …

Biomolecular modeling thrives in the age of technology

T Schlick, S Portillo-Ledesma - Nature computational science, 2021 - nature.com
The biomolecular modeling field has flourished since its early days in the 1970s due to the
rapid adaptation and tailoring of state-of-the-art technology. The resulting dramatic increase …

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

F Noé, C Schütte, E Vanden-Eijnden… - Proceedings of the …, 2009 - National Acad Sciences
Characterizing the equilibrium ensemble of folding pathways, including their relative
probability, is one of the major challenges in protein folding theory today. Although this …