Practical Cheminformatics

MARCH 28, 2022

Anyway, I used a method similar to the one described in this blog post , which exploits the AllChem.AssignBondOrdersFromTemplate method in the RDKit. Cluster the fragment structures Readers of this blog probably know about my fondness for Self-Organizing Maps (SOMs), which I wrote about here and here.

Fragment Screening 52

Fragment Screening Screening Hits 52

Molecular Design

MAY 26, 2020

|| next >> It’s been ages since the last blog post. However, I do realize that many people only follow the blog for the April Fools posts so I’ll link them here for easy reference [ 2013 | 2015 | 2016 | 2017 | 2018 | 2019 ]. Martin and I wrote a short article which we uploaded to figshare and Martin also did a blog post.

Fragment Screening 52

Fragment Screening Drugs 52

Molecular Design

JANUARY 12, 2021

> It’s been ages since my last COVID-19 post (How not to repurpose a 'drug') and I’ll kick blogging off for 2021 with a follow up to an even older post (SARS-CoV-2 main protease. Crowdsourcing, peptidomimetics and fragments).

Fragment Screening 52

Fragment Screening Treatment Nurses Doctors 52

Molecular Design

JULY 18, 2020

A number of peptidomimetic Mpro inhibitors have been described in the literature and this blog post by Chris Southan may be of interest. It’s also worth mentioning that fragment screens have been run against SARS-CoV-2 Nsp3 macrodomain at UCSF and Diamond since there are no known inhibitors for this target.

Biochemical Assays 52

Biochemical Assays Fragment Screening Pharmacokinetics Drugs 52

Dark Matter Blog

APRIL 4, 2023

We sampled several screening platforms in the course of our efforts, including fragment screening using ligand-observed nuclear magnetic resonance (NMR), DNA-encoded libraries (DEL), and SEC-MS. Each of these platforms is thoroughly vetted in protein world, but using them on RNA can yield surprising results.

Small Molecule 52

Small Molecule RNA Fragment Screening DNA 52

PerkinElmer

JUNE 3, 2022

The second virtual screen focused on optimization of a hit from a previous crystallographic fragment screen. Fragment-to-lead optimization was guided by searches in a library of millions of compounds combined with docking screens to select the best candidate. Journal of the American Chemical Society.

Fragment Screening 52

Fragment Screening Clinical Trials Vaccine Pharmacokinetics 52

Molecular Design

AUGUST 2, 2020

Paramin panorama Crystallographic fragment screens have been run recently against the main protease (at Diamond ) and the Nsp3 macrodomain (at UCSF and Diamond ) of SARS-Cov-2 and I thought that it might be of interest to take a closer look at why we screen fragments.

Fragment Screening 40

Fragment Screening Computational Chemistry Engineering Drugs 40