Inter-residue distances surrounding the ligand data sets using MANORAA
Description
Distances measured between distinctive parts of amino acid residues surrounding the ligand.
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Steps to reproduce
Data S1 was created by using the ligand's heteroatoms for superposition to find distances among frequently occurring atoms of the residues for 180 ligands (PDB-3 letter codes) data sets. A more precise calculation at Manoraa.org is required by adding more atoms along the core of the structure for superposition if the ligand of interest is flexible. Examples of the more precise superposition along the ligands' core results in distance tables for TOP-DHFR in Data S2 and MTX-DHFR in Data S3. For more details, please read our article: Tanramluk D, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtananku J, Narupiyakul L, Akavipat R, Yuvaniyama J. MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure (2021).