Rational design in photopharmacology with molecular photoswitches

P Kobauri, FJ Dekker, W Szymanski… - Angewandte …, 2023 - Wiley Online Library
Photopharmacology is an attractive approach for achieving targeted drug action with the use
of light. In photopharmacology, molecular photoswitches are introduced into the structure of …

Learning molecular representations for medicinal chemistry: miniperspective

KV Chuang, LM Gunsalus… - Journal of Medicinal …, 2020 - ACS Publications
The accurate modeling and prediction of small molecule properties and bioactivities depend
on the critical choice of molecular representation. Decades of informatics-driven research …

Molecular graph convolutions: moving beyond fingerprints

S Kearnes, K McCloskey, M Berndl, V Pande… - Journal of computer …, 2016 - Springer
Molecular “fingerprints” encoding structural information are the workhorse of
cheminformatics and machine learning in drug discovery applications. However, fingerprint …

Molecular recognition in chemical and biological systems

E Persch, O Dumele, F Diederich - … Chemie International Edition, 2015 - Wiley Online Library
Abstract Structure‐based ligand design in medicinal chemistry and crop protection relies on
the identification and quantification of weak noncovalent interactions and understanding the …

Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17

L Ruddigkeit, R Van Deursen, LC Blum… - Journal of chemical …, 2012 - ACS Publications
Drug molecules consist of a few tens of atoms connected by covalent bonds. How many
such molecules are possible in total and what is their structure? This question is of pressing …

Pharmit: interactive exploration of chemical space

J Sunseri, DR Koes - Nucleic acids research, 2016 - academic.oup.com
Abstract Pharmit (http://pharmit. csb. pitt. edu) provides an online, interactive environment for
the virtual screening of large compound databases using pharmacophores, molecular …

Practical aspects of free-energy calculations: a review

N Hansen, WF Van Gunsteren - Journal of chemical theory and …, 2014 - ACS Publications
Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …

Defining levels of automated chemical design

B Goldman, S Kearnes, T Kramer, P Riley… - Journal of medicinal …, 2022 - ACS Publications
One application area of computational methods in drug discovery is the automated design of
small molecules. Despite the large number of publications describing methods and their …

The symbiotic relationship between drug discovery and organic chemistry

OO Grygorenko, DM Volochnyuk… - … A European Journal, 2020 - Wiley Online Library
All pharmaceutical products contain organic molecules; the source may be a natural product
or a fully synthetic molecule, or a combination of both. Thus, it follows that organic chemistry …

Rational approaches to improving selectivity in drug design

DJ Huggins, W Sherman, B Tidor - Journal of medicinal chemistry, 2012 - ACS Publications
Appropriate tuning of binding selectivity is a primary objective in the discovery and
optimization of a compound on the path toward developing a drug. The environment in …