TY - JOUR

T1 - X-ray crystallography module in MD simulation program Amber 2023. Refining the models of protein crystals

AU - Михайловский, Олег Владимирович

AU - Измайлов, Сергей Александрович

AU - Xue, Yi

AU - Case, David A.

AU - Скрынников, Николай Русланович

PY - 2023/12/26

Y1 - 2023/12/26

N2 - The MD simulation package Amber offers an attractive platform to refine crystallographic structures of proteins: (i) state-of-the-art force fields help to regularize protein coordinates and reconstruct the poorly diffracting elements of the structure, such as flexible loops; (ii) MD simulations restrained by the experimental diffraction data provide an effective strategy to optimize structural models of protein crystals, including explicitly modeled interstitial solvent as well as crystal contacts. Here we present the new crystallography module xray, released as a part of the Amber 2023 package. This module contains functions to calculate and scale structure factors (including the contributions from bulk solvent), evaluate the maximum-likelihood-type crystallographic potential and compute its derivative forces. The X-ray functionality of Amber no longer relies on external dependencies, so that the full advantage of GPU acceleration can be taken. This makes it possible to refine in a short time hundreds of crystal models, including supercell models comprised of multiple unit cells. The new automated Amber-based refinementprocedure leads to an appreciable improvement in 푅푓푟푒푒 (in some cases, by as much as 0.067) as well as MolProbity scores.

AB - The MD simulation package Amber offers an attractive platform to refine crystallographic structures of proteins: (i) state-of-the-art force fields help to regularize protein coordinates and reconstruct the poorly diffracting elements of the structure, such as flexible loops; (ii) MD simulations restrained by the experimental diffraction data provide an effective strategy to optimize structural models of protein crystals, including explicitly modeled interstitial solvent as well as crystal contacts. Here we present the new crystallography module xray, released as a part of the Amber 2023 package. This module contains functions to calculate and scale structure factors (including the contributions from bulk solvent), evaluate the maximum-likelihood-type crystallographic potential and compute its derivative forces. The X-ray functionality of Amber no longer relies on external dependencies, so that the full advantage of GPU acceleration can be taken. This makes it possible to refine in a short time hundreds of crystal models, including supercell models comprised of multiple unit cells. The new automated Amber-based refinementprocedure leads to an appreciable improvement in 푅푓푟푒푒 (in some cases, by as much as 0.067) as well as MolProbity scores.

U2 - 10.1021/acs.jcim.3c01531

DO - 10.1021/acs.jcim.3c01531

M3 - Article

JO - Journal of Chemical Information and Modeling

JF - Journal of Chemical Information and Modeling

SN - 1549-9596

ER -