The "small molecule universe" (SMU), the set of all synthetically feasible organic molecules of 500 Da molecular weight or less, is estimated to contain over 10(60) structures, making exhaustive searches for structures of interest impractical. Here, we describe the construction of a "representative universal library" spanning the SMU that samples the full extent of feasible small molecule chemi...

BindingDB collects measured binding affinities of proteins and small molecules that bind via noncovalent interactions, in order to help scientists design new medications. This document provides background information on protein-small molecule binding, drug design, and the measurement of binding affinities. Subsequent documents will discuss the data that BindingDB collects and how BindingDB may ...

Molecule optimization is a fundamental task for accelerating drug discovery, with the goal of generating new valid molecules that maximize multiple properties while maintaining similarity to input molecule. Existing generative models and reinforcement learning approaches made initial success, but still face difficulties in simultaneously optimizing properties. To address such challenges, we pro...

The storage capacity of hydrogen on Na-decorated born nitride nanotubes (BNNTs) is investigated by using density functional theory within Quantum Espresso and Gaussian 09. The results obtained predict that a single Na atom tends to occupy above the central region of the hexagonal rings in (5,0) and (3,3) BNNT structures with a binding energy of -2.67 and -4.28 eV/Na-atom respectively. When a si...

The present paper aims to investigate the role of open metal site metal-organic frameworks (MOFs) on hydrogen adsorptivity using periodic boundary condition (PBC) density functional theory (DFT). Hence, MIL-47-M (M = V and Fe) were selected and one hydrogen molecule adsorptivity was calculated in different orientations on them. Four different chemical sites were identified in every cluster sect...

We present a theory for analyzing residence times of single molecules in fixed detection area scanning tunneling microscope (STM). The approach is developed one-dimensional molecule diffusion and can be extended to two dimensions by using the same methodology. Explicit results are derived an harmonic attractive repulsive tip-molecule interaction. Applications allows one estimate type strength i...