Recent developments in free energy calculations for drug discovery
The grand challenge in structure-based drug design is achieving accurate prediction of
binding free energies. Molecular dynamics (MD) simulations enable modeling of …
binding free energies. Molecular dynamics (MD) simulations enable modeling of …
[HTML][HTML] Recent developments in multiscale free energy simulations
Physics-based free energy simulations enable the rigorous calculation of properties, such as
conformational equilibria, solvation or binding free energies. While historically most …
conformational equilibria, solvation or binding free energies. While historically most …
Accurate binding free energy method from end-state MD simulations
E Akkus, O Tayfuroglu, M Yildiz… - Journal of Chemical …, 2022 - ACS Publications
Herein, we introduce a new strategy to estimate binding free energies using end-state
molecular dynamics simulation trajectories. The method is adopted from linear interaction …
molecular dynamics simulation trajectories. The method is adopted from linear interaction …
Molecular simulations of conformational transitions within the insulin receptor kinase reveal consensus features in a multistep activation pathway
Modulating the transitions between active and inactive conformations of protein kinases is
the primary means of regulating their catalytic activity, achieved by phosphorylation of the …
the primary means of regulating their catalytic activity, achieved by phosphorylation of the …
Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m6A) Recognition by the Reader Domain of YTHDC1
N6-Methyladenosine (m6A) is the most frequent modification in eukaryotic messenger RNA
(mRNA) and its cellular processing and functions are regulated by the reader proteins …
(mRNA) and its cellular processing and functions are regulated by the reader proteins …
Efficient alchemical intermediate states in free energy calculations using λ-enveloping distribution sampling
Alchemical free energy calculations generally require intermediate states along a coupling
parameter λ to establish sufficient phase space overlap for obtaining converged results …
parameter λ to establish sufficient phase space overlap for obtaining converged results …
Deciphering nucleotide modification-induced structure and stability changes
T Hurst, SJ Chen - RNA biology, 2021 - Taylor & Francis
Nucleotide modification in RNA controls a bevy of biological processes, including RNA
degradation, gene expression, and gene editing. In turn, misregulation of modified …
degradation, gene expression, and gene editing. In turn, misregulation of modified …
Variational method for networkwide analysis of relative ligand binding free energies with loop closure and experimental constraints
TJ Giese, DM York - Journal of chemical theory and computation, 2021 - ACS Publications
We describe an efficient method for the simultaneous solution of all free energies within a
relative binding free-energy (RBFE) network with cycle closure and experimental/reference …
relative binding free-energy (RBFE) network with cycle closure and experimental/reference …
Development of Multiscale Force Field for Actinide (An3+) Solutions
A multiscale force field (FF) is developed for an aqueous solution of trivalent actinide cations
An3+ (An= U, Np, Pu, Am, Cm, Bk, and Cf) by using a 12-6-4 Lennard-Jones type potential …
An3+ (An= U, Np, Pu, Am, Cm, Bk, and Cf) by using a 12-6-4 Lennard-Jones type potential …
Robust, efficient and automated methods for accurate prediction of protein-ligand binding affinities in AMBER Drug Discovery Boost
Recent concurrent advances in methodology development, computer hardware and
simulation software has transformed our ability to make practical, quantitative predictions of …
simulation software has transformed our ability to make practical, quantitative predictions of …