We present {four|4} tree-based machine {learning|studying|understanding|finding out|mastering} models for protein pKa prediction. The {four|4} models, Random Forest, {Extra|Additional|Added|Further} Trees, {extreme|intense} Gradient Boosting (XGBoost) and Light Gradient Boosting Machine (LightGBM), {were|had been|have been} {trained|educated} on {three|3} experimental PDB and pKa datasets, two of which {included|integrated|incorporated} a notable portion of internal residues. We observed {similar|comparable|equivalent|related} {performance|overall performance|efficiency|functionality} {among|amongst} the {four|4} machine {learning|studying|understanding|finding out|mastering} algorithms. {The best|The very best|The most effective|The top|The ideal|The most beneficial} model {trained|educated} {on the|around the} {largest|biggest} dataset performs 37% {better|much better|far better|greater|superior|improved} than the {widely|extensively|broadly} {used|utilized|employed|utilised|applied|made use of} empirical pKa prediction tool PROPKA. The {overall|general|all round} RMSE for this model is 0.69, with surface and buried RMSE values {being|becoming|getting} 0.56 and 0.78, respectively, {considering|contemplating|thinking about|taking into consideration|thinking of} six residue {types|kinds|varieties|sorts|forms} (Asp, Glu, His, Lys, Cys and Tyr), and 0.63 when {considering|contemplating|thinking about|taking into consideration|thinking of} Asp, Glu, His and Lys only. We {provide|offer|supply|give|present|deliver} pKa predictions for proteins in human proteome {from the|in the} AlphaFold Protein Structure Database and observed that 1% of Asp/Glu/Lys residues have {highly|extremely|very|hugely} shifted pKa values close {to the|towards the|for the} physiological pH. Price of 5-Bromobenzene-1,3-diamine Formula of Methyltetrazine-Amine PMID:24455443
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