Spinning coral

Binding Site Comparison Benchmarks - II - Binding sites on the similar proteins

pocket comparison

structure-based drug design

Second post on establishing a benchmark for binding site comparison methods on similar proteins

Peter Schmidtke

Forced revamp ongoing

This blog is under migration to quarto.

Peter Schmidtke

Binding Site Comparison Benchmarks - I - Binding sites on the same protein

pocket comparison

structure-based drug design

First post in a row on setting up a proper benchmark dataset for binding site comparison algorithm evaluation.

Peter Schmidtke

Binding site comparison - current benchmark issues

pocket comparison

structure-based drug design

A (long) comment on current pitfalls on binding site comparison papers & their benchmarking

Torsion angle scan with rdkit & xtb

Log of the hassle doing torsion angle scans with rdkit & xtb - ultimately comparing results to the crystallography open database

Peter Schmidtke

fpocket 4.0 - Towards biologics

A quick demo of all the new fpocket features with special focus on protein-peptide interfaces

Peter Schmidtke

Crystallography Open Database and torsion angle statistics with rdkit

crystallography

small molecule xray

First steps to check how easy / feasible it is to extract torsion angle statistics from the COD

Peter Schmidtke

Grafting fragments onto molecules in rdkit - babysteps

This is a quick set-up for attaching a fragment to a molecule on a particular location.

Peter Schmidtke