ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins

D Song, W Wang, W Ye, D Ji, R Luo… - Chemical biology & …, 2017 - Wiley Online Library
… acids, and other amino acids remain the same to that of the previous force field ff14SB. …
for each protein with ff14IDPs and ff14SB force fields. The secondary chemical shift and other …

phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids

LE Raguette, AE Cuomo, KAA Belfon… - Journal of Chemical …, 2024 - ACS Publications
The overarching goal of this work is to extend the ff14SB treatment to … in this work and
retain the same dihedral parameters as ff14SB; those not present in ff14SB were trained here (…

ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB

JA Maier, C Martinez, K Kasavajhala… - Journal of chemical …, 2015 - ACS Publications
… cost of destabilizing β structures, we also simulated a short β-hairpin system to evaluate
the ability of the force field to provide balance in sequence-dependent secondary structure …

FF12MC: A revised AMBER forcefield and new protein simulation protocol

YP Pang - Proteins: Structure, Function, and Bioinformatics, 2016 - Wiley Online Library
… Statistical survival analysis shows that FF12MC folds chignolin and CLN025 in isobaric–isothermal
MD simulations 2–4 times faster than FF14SB under the same protein simulation …

Combined fragment-based machine learning force field with classical force field and its application in the NMR calculations of macromolecules in solutions

K Liao, S Dong, Z Cheng, W Li, S Li - Physical Chemistry Chemical …, 2022 - pubs.rsc.org
… MM force field for macromolecules in solutions by combining the GEBF-NN force field for the
solute molecule and ff14SB force field for … In this work, the ff14SB force field calculations and …

ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution

C Tian, K Kasavajhala, KAA Belfon… - Journal of chemical …, 2019 - ACS Publications
… We continue our previous philosophy for the Amber “SB” (Stony Brook) force fields, … The
second difference from ff14SB is that we address the polarization inconsistency during dihedral …

Assessing AMBER force fields for protein folding in an implicit solvent

Q Shao, W Zhu - Physical Chemistry Chemical Physics, 2018 - pubs.rsc.org
… (FF99SBildn, FF99SBnmr, FF12SB, FF14ipq, FF14SB, and FF14SBonlysc) as coupled with
a … We evaluated the force fields in the implicit solvent from two aspects: the conformational …

The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins

D Song, R Luo, HF Chen - Journal of chemical information and …, 2017 - ACS Publications
… with the base generic force field and also our previous ff14IDPs that only corrects the eight
… Apparently users must choose ff14SB as the generic protein force field to use the database …

Conformational landscapes of artificial peptides predicted by various force fields: are we ready to simulate β-amino acids?

J Park, HS Lee, H Kim, JM Choi - Physical Chemistry Chemical Physics, 2023 - pubs.rsc.org
… , the performance of conventional force fields in predicting the … three popular force fields,
AMBER ff14SB, CHARMM36m, and … the energy landscape of each force field and assess the

Disagreement between the structure of the dTpT thymine pair determined by NMR and molecular dynamics simulations using amber 14 force fields

C Nganou, SD Kennedy… - The Journal of Physical …, 2016 - ACS Publications
… ) for the 5′-sugar and significant flexibility of C3′ of the 3′-… the current AMBER force field
does not accurately predict thethe results of the REMD simulation using both the ff14SB and …