Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters

INTERACTION OF PROTEINS WITH SMALL MOLECULES

PDBeChem: Searching for small molecules and small molecule fragments

Proteins Chemical biology Structures Beginner 1 hour PDBeChem allows you to search for chemical components (ligands, small molecules and monomers) that appear in PDB entries, and discover which protein structures bind a particular ligand. This course will show you how to use PDBeChem and what you can do with it. An undergraduate degree in a life science subject would be an advantage. You may wi...

Characterizing protein domain associations by Small-molecule ligand binding.

BACKGROUND Protein domains are evolutionarily conserved building blocks for protein structure and function, which are conventionally identified based on protein sequence or structure similarity. Small molecule binding domains are of great importance for the recognition of small molecules in biological systems and drug development. Many small molecules, including drugs, have been increasingly id...

Characterizing non-covalent nucleic acid interactions with small molecules and proteins by calorimetry

The expression or replication of genes is affected by the binding of small molecule ligands and proteins to nucleic acid sequences. Such binding events are critical for the physiological integrity of organisms and therefore are of fundamental interest to life scientists. Recently, the thermodynamics driving these interactions have also become important to pharmaceutical scientists investigating...

Ligandbook: an online repository for small and drug-like molecule force field parameters

Summary Ligandbook is a public database and archive for force field parameters of small and drug-like molecules. It is a repository for parameter sets that are part of published work but are not easily available to the community otherwise. Parameter sets can be downloaded and immediately used in molecular dynamics simulations. The sets of parameters are versioned with full histories and carry u...