Distribution of reciprocal of interatomic distances: A fast structural metric

T Zhou, A Caflisch - Journal of chemical theory and computation, 2012 - ACS Publications
We present a structural metric based on the Distribution of Reciprocal of Interatomic
Distances (DRID) for evaluating geometrical similarity between two conformations of a …

Relationships between molecular complexity, biological activity, and structural diversity

A Schuffenhauer, N Brown, P Selzer… - Journal of chemical …, 2006 - ACS Publications
Following the theoretical model by Hann et al. moderately complex structures are preferable
lead compounds since they lead to specific binding events involving the complete ligand …

Structural protein descriptors in 1-dimension and their sequence-based predictions

L Kurgan, F Miri Disfani - Current Protein and Peptide Science, 2011 - ingentaconnect.com
The last few decades observed an increasing interest in development and application of 1-
dimensional (1D) descriptors of protein structure. These descriptors project 3D structural …

Combining machine learning and quantum mechanics yields more chemically aware molecular descriptors for medicinal chemistry applications

S Tortorella, E Carosati, G Sorbi, G Bocci… - Journal of …, 2021 - Wiley Online Library
Molecular interaction fields (MIFs), describing molecules in terms of their ability to interact
with any chemical entity, are one of the most established and versatile concepts in drug …

How similar are those molecules after all? Use two descriptors and you will have three different answers

A Bender - Expert opinion on drug discovery, 2010 - Taylor & Francis
Importance of the field: Molecular similarity searching (ligand-based virtual screening) is one
of the routine computational techniques used in drug discovery and pharmacological …

A novel index for the description of molecular linearity

H Patel, MTD Cronin - Journal of Chemical Information and …, 2001 - ACS Publications
To investigate the description of molecular shape, a heterogeneous data set of 200
compounds was designed. The compounds included many disparate molecular shapes …

Discriminative chemical patterns: automatic and interactive design

S Bietz, KT Schomburg, M Hilbig… - Journal of chemical …, 2015 - ACS Publications
The classification of molecules with respect to their inhibiting, activating, or toxicological
potential constitutes a central aspect in the field of cheminformatics. Often, a discriminative …

Mapping ligand-shape space for protein–ligand systems: Distinguishing key-in-lock and hand-in-glove proteins

J Zarnecka, I Lukac, SJ Messham… - Journal of Chemical …, 2021 - ACS Publications
Many of the recently developed methods to study the shape of molecules permit one
conformation of one molecule to be compared to another conformation of the same or a …

Molecular descriptors in chemoinformatics, computational combinatorial chemistry, and virtual screening

L Xue, J Bajorath - Combinatorial chemistry & high throughput …, 2000 - ingentaconnect.com
Many contemporary applications in computer-aided drug discovery and chemoinformatics
depend on representations of molecules by descriptors that capture their structural …

PyL3dMD: Python LAMMPS 3D molecular descriptors package

P Panwar, Q Yang, A Martini - Journal of Cheminformatics, 2023 - Springer
Molecular descriptors characterize the biological, physical, and chemical properties of
molecules and have long been used for understanding molecular interactions and …