yufengwhy

good questions but no related open datasets

Last answer remind me of a SIGIR 17 paper (Evaluating Web Search with a Bejeweled Player Model)

1. How to config to produce EquiBind-R and EquiBind-U? EquiBind-U is EquiBind w/o 3.2.2 when inference? EquiBind-R is to input the PDBBind conformer to EquiBind and only learn rotation and...

@luwei0917 The model outputs the same affinity value for different structures of the same ligand: RDKit structure, PDBBind structure and predict structures of TankBind. Is this normal?

@luwei0917 That sounds awesome. I am curious about how tankbind achieve that the predicted affinity is conformation-agnostic, that is, the input of coordinates of ligands do not influence the outputted...

@luwei0917 1. predict coord D^c_{j,k} in Equation (5) is the group truth distance from PDBBind? If so, the label is leaked? 2. predict affinity D_{ij} in L_distance around Equation (4)...

@luwei0917 1. "It is based on the RDKit generated conformation when testing or inferencing." This will make the conformation closer to RDKit, i.e., farther to PDB conformation？

@luwei0917 Is TankBind SE(3)-equivariant？

> The LAS mask exists in self dock. therefore, only the basic constraint is imposed. The general conformation is determined by the interaction. LAS includes rings, and the N-O-C ring...

protein's GVP embedding and ligand's torchdrug feature, is these features invariant or equivariant?