Interaction Perception

G. Cavallo, P. Metrangolo, R. Milani, T. Pilati, A. Priimagi, G. Resnati, and G. Terraneo,
The Halogen Bond
Chemical Reviews Vol. 116 no. 4, pp. 2478-–2601, 2016
C. Bissantz, B. Kuhn, and M. Stahl,
A medicinal chemist’s guide to molecular interactions,
Journal of Medicinal Chemistry Vol. 53 no. 14, pp. 5061–5084, 2010
S. Kuma and R. Nussinov,
Relationship between ion pair geometries and electrostatic strengths in proteins,
Biophysical Journal, Vol. 83 no. 3, pp. 1595–-1612, 2002.
G. Marcou, and D. Rognan,
Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
Journal of Chemical Information and Modeling Vol. 47 no. 1, pp. 195–-207, 2007


Guy W. Bemis and Mark A. Murcko,
The Properties of Known Drugs. 1. Molecular Frameworks,
Journal of Medicinal Chemistry, Vol. 39, pp. 2887–2893 1996,
Lipinski, C.A., Lombardo, F., Dominy, B.W. and Feeney, P.J.,
Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings,
Advanced Drug Delivery Reviews, Vol. 23, pp. 3-25, 1997

Validating Protein-Ligand Structures

G. L.Warren, T. D. Do, B. P. Kelley, A. Nicholls, and S. D. Warren,
Essential considerations for using protein-ligand structures in drug discovery
Drug Discovery Today Vol. 17 no. 23–24, pp. 1270–1281, 2012

Ramachandran Plot

Vincent B. Chen, W. Bryan Arendall III, Jeffrey J. Headd, Daniel A. Keedy, Robert M. Immormino, Gary J. Kapral, Laura W. Murray, Jane S. Richardson, David C. Richardson,
MolProbity: all-atom structure validation for macromolecular crystallography.
Acta Crystallographica, D66, pp. 12–21, 2010

Color References

J.E.J. Mills and P.M. Dean,
Three-dimensional hydrogen-bond geometry and probability information from a crystal survey,
Journal of Computer-Aided Molecular Design, Vol. 10, pp. 607, 1996.