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, (online: http://www.springerlink.com/content/m7j34558107q3748/?p=bb33f4fc2ac64df8b47314e96619a86d&pi=13)

[Grant-2006]

J. Andrew Grant, James A. Haigh, Barry T. Pickup, Anthony Nicholls and Roger A. Sayle, Lingos, Finite State Machines and Fast Similarity Searching, Journal of Chemical Information and Modeling, Vol. 45, pp. 1912–-1918, 2006, (online: http://pubs.acs.org/doi/abs/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, (online: http://pubs.acs.org/doi/abs/10.1021/ci034231b)

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 (online: http://pubs.acs.org/doi/abs/10.1021/acs.chemrev.5b00484)

[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 (online: http://pubs.acs.org/doi/abs/10.1021/jm100112j)

[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. (online: http://dx.doi.org/10.1016/S0006-3495(02)73929-5)

[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 (online: http://pubs.acs.org/doi/abs/10.1021/ci600342e)

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, (online: http://pubs.acs.org/doi/abs/10.1021/jm9602928)

[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 (online: http://pubs.acs.org/doi/abs/10.1021/ci100297y)

[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. (online: http://pubs.acs.org/doi/abs/10.1021/ci9601675)

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 (online: https://doi.org/10.1016/j.drudis.2012.06.011)

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 (online: https://www.ncbi.nlm.nih.gov/pubmed/20057044)

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.