pH condition for MD traj Dataset

使用的是中性条件 

“For convenience, the “standard” protonation states at neutral pH were applied to the amino acid residues on the protein side. Thus, Asp, Glu, and His residues were negatively charged, and Arg and Lys residues were positively charged; carboxylic, sulfonic, and phosphoric acid groups in the ligands were built in deprotonated forms, while aliphatic amine groups, guanidine, and amidine groups were built in protonated forms. Neither the protein nor the ligand was subjected to any structural optimization. Therefore, all of the non-hydrogen atoms on both the protein and the ligand molecule retained their original coordinates from PDB.”

使用的是中性条件 pH=7

"Short-length MD simulation was applied to further refine the protein–ligand complex structure. Here, we utilized the AMBER software (version 2014) (30) to carry out the MD simulation tasks. The GAFF force field parameters were applied to the ligand molecule. Its atomic partial charges were derived with the RESP method (31) based on the HF/6-31G* computation results given by the Gaussian software (version 09, released by Gaussian Inc). (32) The protein atoms were assigned according to the FF14SB template charges, and all ionizable residues were set at the default protonation states at pH = 7. The complex structure was then soaked in a cubic box of TIP3P water molecules with a margin of 10 Å along each dimension. Counterions (i.e., Na+ or Cl–) were added to neutralize the whole system."

使用的是中性条件 pH=7

"All the domain structures have been prepared with a standard protonation protocol at pH 7 including charge state assignments, proton placement and H-bond network optimization. Peptide chains were capped with acetylated and N-methylated termini. The systems were solvated in cubic boxes of TIP3P water with at least 9 Å of padding on each side, neutralized, and ionized with Na+ and Cl− ions at 0.150 M concentration. Systems whose resulting solvation cubic box was larger than (100 Å)3 were discarded. The final dataset includes 5,398 accepted domains, as illustrated in Fig. 1. HTMD version 1.16 was used for all the building steps"

未见提及体系准备的pH条件的MD数据集：

MISATO：MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery | Nature Computational Science

ATLAS：ATLAS: protein flexibility description from atomistic molecular dynamics simulations | Nucleic Acids Research | Oxford Academic

MemProtMD：MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions | Nucleic Acids Research | Oxford Academic

SCoV2-MD： SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions | Nucleic Acids Research | Oxford Academic

MoDEL：MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories: Structure

Dynamic PDB：     arXiv:2408.12413