BucketListPapers 31/100: SMILES: A lightweight method of structure notation

  We are blessed in modern cheminformatics that several options exist for chemical structural representation within computer software and databases. These days we almost...

BucketListPapers 32/100: The next step in representing molecules as a single number – Extended-Connectivity Fingerprints

We highlighted one of the first papers describing a method to represent chemical structures in a computer as a unique fingerprint. Fingerprints allow very...

BucketListPapers 33/100: Two papers discussing Molecular Similarity. They are different, honest.

Molecular similarity is an important concept, and vital for rapid database searching and activities like clustering that are critical for day to day working...

BucketListPapers 34/100: How do we define a ‘scaffold’ in medchem? How do you get a computer to do it?

Another easy thing for medicinal chemists to talk about is the ‘scaffold’ of the molecule, or indeed ‘scaffold hopping’. Between chemists it might be...

BucketListPapers 35/100: Chemical Structure Checking – essential hygiene for chemists

This paper should be compulsory reading for every chemist who ever creates a chemical structure that could end up in a database just so...

BucketListPapers 36/100: Critical reading for Fluorine fans

  Most medicinal chemists know that fluorine is the “wild-child” of the halogens, shifting adjacent pKa’s and blocking metabolism.  This paper however is a...

BucketListPapers 37/100 Tuning Amines pKa’s : a regular medchem task

Ionisation influences so many of a compound’s properties: solubility, binding to ionic sub-sites, permeability and interactions with critical targets like the hERG ion channel. ...

BucketListPapers 38/100: Open Season on Virtual Screening Compounds

When starting a drug(or agrochemical) hunting program one of the first vital steps is having compounds that bind to your target. Getting to this...

BucketListPapers 39/100: getting a view on ligand protein interactions

  Ligand:protein interactions are intrinsically difficult to view, three dimensional  and highly complex.  Picking out the critical interactions can be an exercise in rotating...

BucketListPapers 40/100: The instant 3D structure revolution

Generating three dimensional structures of molecules from the 2D structure is a classic computational chemistry problem. To generate the best possible structure requires quantum...