Molecular similarity: a key technique in molecular informatics

A Bender, RC Glen - Organic & biomolecular chemistry, 2004 - pubs.rsc.org
Molecular Informatics utilises many ideas and concepts to find relationships between
molecules. The concept of similarity, where molecules may be grouped according to their …

New methodologies for ligand-based virtual screening

FL Stahura, J Bajorath - Current pharmaceutical design, 2005 - ingentaconnect.com
Computational screening of compound databases has become increasingly popular in
pharmaceutical research. Virtual screening approaches can roughly be divided into target …

How fast-folding proteins fold

K Lindorff-Larsen, S Piana, RO Dror, DE Shaw - Science, 2011 - science.org
An outstanding challenge in the field of molecular biology has been to understand the
process by which proteins fold into their characteristic three-dimensional structures. Here …

Exploiting manifold geometry in hyperspectral imagery

CM Bachmann, TL Ainsworth… - IEEE transactions on …, 2005 - ieeexplore.ieee.org
A new algorithm for exploiting the nonlinear structure of hyperspectral imagery is developed
and compared against the de facto standard of linear mixing. This new approach seeks a …

Generative topographic mapping (GTM): universal tool for data visualization, structure‐activity modeling and dataset comparison

N Kireeva, II Baskin, HA Gaspar, D Horvath… - Molecular …, 2012 - Wiley Online Library
Here, the utility of Generative Topographic Maps (GTM) for data visualization, structure‐
activity modeling and database comparison is evaluated, on hand of subsets of the …

Fast, efficient fragment-based coordinate generation for Open Babel

N Yoshikawa, GR Hutchison - Journal of cheminformatics, 2019 - Springer
Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task for
cheminformatics and across a wide range of molecular modeling. Consequently, developing …

SyGMa: combining expert knowledge and empirical scoring in the prediction of metabolites

L Ridder, M Wagener - ChemMedChem: Chemistry Enabling …, 2008 - Wiley Online Library
Predictions of potential metabolites based on chemical structure are becoming increasingly
important in drug discovery to guide medicinal chemistry efforts that address metabolic …

General melting point prediction based on a diverse compound data set and artificial neural networks

M Karthikeyan, RC Glen, A Bender - Journal of chemical …, 2005 - ACS Publications
We report the development of a robust and general model for the prediction of melting
points. It is based on a diverse data set of 4173 compounds and employs a large number of …

A survey of manifold learning for images

R Pless, R Souvenir - IPSJ Transactions on Computer Vision and …, 2009 - jstage.jst.go.jp
Many natural image sets are samples of a low-dimensional manifold in the space of all
possible images. Understanding this manifold is a key first step in understanding many sets …

Comparative analysis of pharmacophore screening tools

MPA Sanders, AJM Barbosa, B Zarzycka… - Journal of chemical …, 2012 - ACS Publications
The pharmacophore concept is of central importance in computer-aided drug design
(CADD) mainly because of its successful application in medicinal chemistry and, in …