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]

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,

(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,

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[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.

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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

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Peptide Informatics

[Zhang-2012]

Tianhong Zhang; Hongli Li; Hualin Xi; Robert V. Stanton; Sergio H. Rotstein

HELM: A Hierarchical Notation Language for Complex Biomolecule Structure Representation

J. Chem. Inf. Model. 2012, 52 (10), 2796−2806.

DOI: https://pubs.acs.org/doi/10.1021/ci3001925

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

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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.