Bibliography
Fingerprint Similarity Search
[Briem-Lessel-2000]
H, Briem and U. F. Lessel,
In Vitro and in Silico Affinity Fingerprints: Finding Similarities Beyond Structural Classes,
Perspectives in Drug Discovery and Design, Vol. 20, pp. 231–244, 2000,
[Grant-2006]
Grant, J.A.; Haigh, J.A.; Pickup, B.T.; Nicholls, A.; Sayle, R.A.
Lingos, Finite State Machines, and Fast Similarity Searching.
J. Chem. Inf. Model. 2006, 45 (5), 1912–1918.
DOI: 10.1021/ci6002152
[Hert-Willett-2004]
J. Hert, P. Willett and D. J. Wilton
Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures,
Journal of Chemical Information and Computer Science, Vol. 44, pp. 1177–1185 2004,
Interaction Perception
[Cavallo-2016]
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
[Bissantz-2010]
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
[Kumar-2002]
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.
[Marcou-2007]
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
Drug-likeness
[Bemis-1996]
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-1997]
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
Maximum Common Substructure Search
[Hariharan-2011]
R. Hariharan, A. Janakiraman, R. Nilakantan†, B. Singh†, S. Varghese†, G. Landrum, and A. Schuffenhauer,
MultiMCS: A Fast Algorithm for the Maximum Common Substructure Problem on Multiple Molecules
Journal of Chemical Information and Modeling, Vol, 51, pp. 788–-806, 2011
[Raymond-2002]
J. W. Raymond, and P. Willett,
Maximum common subgraph isomorphism algorithms for the matching of chemical structures
Journal of Computer-Aided Molecular Design, Vol. 16, pp. 521–-533, 2002
(online: https://doi.org/10.1023/A:1021271615909)
[Wang-1997]
T. Wang, and J. Zhou,
EMCSS: A New Method for Maximum Common Substructure Search,
Journal of Chemical Information and Computer Science, Vol. 37 pp. 828–834, 1997.
Validating Protein-Ligand Structures
[Warren-2012]
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-2010]
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
[MillsDean-1996]
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.