The MedChemica Bucket List
100 Papers Every Medicinal and Computational Chemist Should Read
BucketListPapers 81/100: Pair up your atoms….
The concept of using pairs of atoms and how far apart they are as a way to encode structures underpins many of the grouping...
BucketListPapers 82/100: Hydrogen Bonds – not all the same!
Although Lipinski’s rules and related approaches demand that we count any hydrogen bond donor or acceptor (defined in a rather limited way) as equivalent, there...
BucketListPapers 83/100: The amazing Ames test – avoiding mutagens
For a long time, I had assumed that the AMES test was an abbreviation and that it was one of the most brilliant transformations...
BucketListPapers 84/100: CHARMM: may the force (field) be with you!
First conceived in the 1950s and advanced through the latter half of the 20th century, molecular dynamics simulations have become a key branch of...
BucketListPapers 85/100: Amber: The force (field) is strong with this one!
Following on from our previous bucket list release on the CHARMM MD package and force fields, we now choose to introduce Amber, another MD...
BucketListPapers 86/100: A Step Closer to Unlocking the Potential of FEP for Drug Discovery
Free energy perturbation (FEP), a molecular dynamics (MD) simulation technique that involves transforming a model system between two states to calculate the free energy...
BucketListPapers 87/100: The Ramachandran Plot
A protein’s function is inherently linked to its secondary and tertiary structure, which is determined by its amino acid sequence. Understanding the structures of...
BucketListPapers 88/100 : Energising QSAR Models
Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967. Comparative...
BucketListPapers 89/100: How do we find binding pockets in proteins?
Goodford describes, in 1985, a method for probing proteins computationally to find putative binding sites. For budding computational chemists this is a must read....
BucketListPapers 90/100 – Identification of pharmacophores and who is the best?
This bucket list paper draws comparisons between three commercially available pharmacophore generation programs. All three programs are extensively described. The programs are then compared...
