# Bibliography¶

Ring Perception

 [Balducci-1994] Renzo Balducci and Robert S. Pearlman, Efficient Exact Solution of the Ring Perception Problem, Journal of Chemical Information and Computer Science, Vol. 34, pp. 822–831, 1994.
 [Baumer-1991] L. Baumer, G. Sala and G. Sello, Ring Perception in Organic Structures: A New Algorithm for Finding SSSR, Computational Chemistry, Vol. 15, p. 293-299, 1991.
 [Down-1989] Geoffrey M. Downs, Valerie J. Gillet, John D. Holliday and Michael F. Lynch, Review of Ring Perception Algorithms for Chemical Graphs, Journal of Chemical Information and Computer Science, Vol. 29, pp. 172–187, 1989.
 [Figueras-1996] John Figueras, Ring Perception Using Breadth-First Search, Journal of Chemical Information and Computer Science, Vol. 36, pp. 986–991, 1996.
 [Fujita-1988] Shinsaku Fujita, A new algorithm for selection of synthetically important rings. The essential set of essential rings for organic structures, Journal of Chemical Information and Computer Science, Vol. 28, pp. 78–82, 1988.
 [Gasteiger-1979] Johann Gasteiger and Clemens Jochum, An Algorithm for the Perception of Synthetically Important Rings, Journal of Chemical Information and Computer Science, Vol. 29, pp. 43–48, 1979.
 [Hanser-1996] T. Hanser, P. Jauffret, and G. Kaufmann, A new algorithm for exhaustive ring perception in a molecular graph, Journal of Chemical Information and Computer Science, Vol. 36, pp. 1146–1152, 1996.
 [Plotkin-1971] M. J. Plotkin, Mathematical Basis of Ring-Finding Algorithms in CIDS, Journal of Chemical Documentation, Vol. 11, pp. 60–63, 1971.
 [Qian-1990] C. Qian, W. Fisanick D. E. Hartzler and S. W. Chapman, Enhanced Algorithm for Finding Smallest Set of Smallest Rings, Journal of Chemical Information and Computer Science, Vol. 30, pp. 105–110, 1990.
 [Roos-Kozel-1981] Barbara L. Roos-Kozel and William L. Jorgensen, Computer-Aided Mechanistic Evaluation of Organic Reactions. 2. Perception of Rings, Aromaticity and Tautomers, Journal of Chemical Information and Computer Science, Vol. 21, pp. 101–111, 1981.
 [Takahashi-1994] Yoshimasa Takahashi, Automatic extraction of ring substructures from a chemical structure, Journal of Chemical Information and Computer Science, 1994, Vol. 34, pp. 167–170, 1994.
 [Zamora-1979] Antonio Zamora, An Algorithm for Finding the Smallest Set of Smallest Rings, Journal of Chemical Information and Computer Science, Vol. 16, pp. 40–43, 1976.

Aromaticity Perception

 [Lloyd-1996] Douglas Lloyd, What Is Aromaticity?, Journal of Chemical Information and Computer Science, Vol. 36, pp. 442–447, 1996.

Connectivity Perception

 [Baber-1992] Jon C. Baber and Edward E. Hodgkin, Automatic Assignment of Chemical Connectivity to Organic Molecules in the Cambridge Structural Database, Journal of Chemical Information and Computer Science, Vol. 32, pp. 401–406, 1992.
 [Kearsley-1993] Simon K. Kearsley, A Quick Robust Method for Assigning A Kekulé Structure, Computers in Chemistry, Vol. 17, pp. 1–10, 1993.
 [Labute-1996-I] Paul Labute, Automatic Assignment of Bond Order, Journal of the Chemical Computing Group, On-line, May 1996.
 [Meng-1991] Elaine C. Meng and Richard A. Lewis, Determination of Molecular Topology and Atomic Hybridization States from Heavy Atom Coordinates, Journal of Computational Chemistry, Vol. 12, pp. 891–898, 1991.
 [Rippmann-1997] M. Hendlich, F. Rippmann and G. Barnickel, BALI: Automatic Assignment of Bond and Atom Types for Protein Ligands in the Brookhaven Protein Databank, Journal of Chemical Information and Computer Science, Vol. 37, pp. 774–778, 1997.

Stereochemistry Perception

 [Labute-1996-II] Paul Labute, An Efficient Algorithm for the Determination of Topological RS Chirality, Journal of the Chemical Computing Group*,On-line, November 1996.

Molecule Symmetry Perception

 [Shelley-1977] Craig A. Shelley and Morton E. Munk, Computer Perception of Topological Symmetry, Journal of Chemical Information and Computer Science, Vol. 17, pp. 110–113, 1977.
 [Shelley-1979] Craig A. Shelley and Morton E. Munk, An Approach to the Assignment of Canonical Connection Tables and Topological Symmetry Perception, Journal of Chemical Information and Computer Science, Vol. 19, pp. 247–250, 1979.

Substructure Search

 [Figueras-1972] J. Figueras,. Substructure search by set reduction. Journal of Chemical Documentation, Vol. 12 pp. 237–244, 1972.
 [Ullman-1976] J.R. Ullman, An Algorithm for Subgraph Isomorphism, Journal of the Association of Computing Machinery (JACM), Vol. 23, pp. 31–42, 1976.

Molecule Canonicalization

 [Morgan-1965] H.L. Morgan, The Generation of a Unique Machine Description for Chemical Structures Developed at Chemical Abstracts Service, Journal of Chemical Documentation, Vol. 5, pp. 107–113, 1965.
 [Kelley-2003] Brian Kelley, Graph Canonicalization, Dr. Dobb’s Journal, No. 348 (Algorithms), pp. 66–69, 2003.
 [Ihlenfeldt-1994] Wolf Dietrich Ihlenfeldt and Johann Gasteiger, Hash Codes for the Identification and Classification of Molecular Structure Elements, Journal of Computational Chemistry, Vol. 15, pp. 793–813, 1994.
 [InChI-2013] (online: http://www.inchi-trust.org/)

Maximum Common Substructure Search

 [Bunke-2002] Horst Bunke, Pasquale Foggia, C. Guidobaldi, Carlo Sansone and Mario Vento, A Comparison of Algorithms for Maximum Common Subgraph on Randomly Connected Graphs, Lecture Notes In Computer Science (LNCS) 2396, Proceedings of the Joint IAPR International Workshop on Structural, Syntactic and Statistical Pattern Recognition, pp. 123–132, 2002. OEChem’s MCSS is based upon the ‘’space state search’’ method
 [McGregor-1982] James J. McGregor, Backtrack Search Algorithms and the Maximal Common Subgraph Problem, Software – Practice and Experience, Vol. 12, pp. 23–34, 1982.
 [Raymond-2002] W. R. Raymond, E.J. Gardiner, and P. Willett, Rascal: Calculation of Graph Similarity Using Maximum Common Edge Subgraphs, The Computer Journal, Vol. 45, pp. 632–644, 2002
 [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.

Charge Calculation

 [Gasteiger-1978] Johann Gasteiger and M. Marsili, A New Model for Calculating Atomic Charges in Molecules, Tetrahedron Letters, pp. 3181–3184, 1978.
 [Gasteiger-1980] Johann Gasteiger and M. Marsili, Iterative Partial Equalization of Orbital Electronegativity - A Rapid Access to Atomic Charges, Tetrahedron, Vol. 36, pp. 3219–3228, 1980.

Atom Type Assignment

 [ODonnell-1991] T.J. O’Donnell, Shashidar N. Rao, Konrad Koehler, Yvonne C. Martin and Beverley Eccles, A General Approach for Atom-Type Assignment and the Inter-conversion of Molecular Structure Files, Journal of Computational Chemistry, Vol. 12, pp. 209–214, 1991.
 [Bush-1993] Bruce L. Bush and Robert P. Sheridan, PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases, Journal of Chemical Information and Computer Science, Vol. 33, pp. 756–762, 1993.
 [Pedretti-2003] A. Pedretti, L. Villa and G. Vistoli, Atom-type Description Language: A Universal Language to Recognize Atom Types Implemented in the VEGA program, Theoretical Chemistry Accounts, Vol. 109, pp. 229–232, **2003*.
 [Markley-1998] Markley, J.L., Bax, A., Arata, Y., Hilbers, C.W., Kaptein, R., Sykes, B.D., Wright, P.E. and Wüthrich, K., Recommendations for the presentation of NMR structures of proteins and nucleic acids, Pure and Applied Chemistry, Vol. 70, pp. 117–142, 1998.

Molecular Similarity

 [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.
 [Vidal-2005] David Vidal, Michael Thormann, and Miquel Pons, LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities Journal of Chemical Information and Modeling, Vol. 45, pp. 386–393, 2005.
 [Vidal-2006] David Vidal, Michael Thormann, and Miquel Pons, A Novel Search Engine for Virtual Screening of Very Large Databases, Journal of Chemical Information and Modeling, Vol. 46, pp. 836–843, 2006.
 [Willett-1998] P. Willett, Chemical similarity searching, Journal of Chemical Information and Computer Science, Vol. 38 pp. 983–996, 1998.

Molecular Line Notation

 [Ash-1997] Sheila Ash, Malcolm A. Cline, R. Webster Homer, Tad Hurst and Gregory B. Smith, SYBYL Line Notation (SLN): A Versatile Language for Chemical Structure Representation, Journal of Chemical Information and Computer Science, Vol. 37, pp. 71–79, 1997.
 [Weininger-1988] David Weininger, SMILES: A Chemical Language and Information System: 1. Introduction to Methodology and Encoding Rules, Journal of Chemical Information and Computer Science, Vol. 28, pp. 31–36, 1988.
 [Weininger-1989] David Weininger, Arthur Weininger and Joseph L. Weininger, SMILES 2: Algorithm for Generation of Unique SMILES Notation, Journal of Chemical Information and Computer Science, Vol. 29, pp. 97–101, 1989.

Pharmacophore Identification

 [Ting-2000] A. Ting, R. McGuire, A.P. Johnson and S. Green, Expert System Assisted Pharmacophore Identification, Journal of Chemical Information and Computer Science, Vol. 40, pp. 347–353, 2000.

Conformational Analysis

 [Leach-1990] Andrew R. Leach, Daniel P. Dolata and Keith Prout, Automated Conformational Analysis and Structure Generation: Algorithms for Molecular Perception, Journal of Chemical Information and Computer Science, Vol. 30, pp. 316–324, 1990.

Rotamer Libraries

 [Dunbrack-1997] R.L. Dunbrack, Jr., F.E. Cohen, Bayesian statistical analysis of protein side-chain rotamer preferences, Protein Science, Vol. 6 no. 8, pp. 1661–1681, 1997.
 [Lovell-2000] Simon C. Lovell, J. Michael Word, Jane S. Richardson, David C. Richardson, The penultimate rotamer library, Proteins, Vol. 40 no. 3, pp. 389–408, 2000.
 [Hintze-2016] Bradley J. Hintze, Steven M. Lewis, Jane S. Richardson, David C. Richardson, Molprobity’s ultimate rotamer-library distributions for model validation, Proteins, Vol. 84 pp. 1177–1189, 2016.

Ramachandran Plot

 [Ramachandran-1963] G.N. Ramachandran, C. Ramakrishnan, V. Sasisekharan, Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, Vol. 7, pp. 95–99, 1963.
 [Grosse-Kunstleve-2002] R. W. Grosse-Kunstleve, N. K. Sauter, N. W. Moriarty and P. D. Adams, The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework. J. Appl. Cryst., 35, pp. 126-136, 2002.
 [Lovell-2003] Simon C. Lovell, I. W. Davis, W.B. Arendall, P. I. W. De Bakker, J. M. Word, M. G. Prisant, J. S. Richardson, D. C. Richardson, Structure validation by $$C\alpha$$ OERageometry $$\phi$$, $$\psi$$ and $$C\beta$$ deviation. Proteins, Vol. 50 pp. 437–450, 2003.
 [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.

Sequence Alignment

 [Dayhoff-1978] M.O. Dayhoff, R.M. Schwartz, and B.C. Orcott A model of evolutionary change in proteins, M.O. Dayhoff(ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington, DC, Vol. 5, pp 345–352, 1978.
 [Gonnet-1992] G.H. Gonnet, M.A. Cohen, and S.A. Benner, Exhaustive matching of the entire protein sequence database, Science, Vol. 256 no. 5062, pp. 1443–1445, 1992.
 [Henikoff-1992] S. Henikoff and J.G. Henikoff, Amino acid substitution matrices from protein blocks, Proceedings of the National Academy of Science, USA, Vol. 89 no. 22, pp. 10915–10919, 1992.

Interaction Perception

 [Kumar-2002] S. Kumar and R. Nussinov, Relationship between ion pair geometries and electrostatic strengths in proteins, Biophysical Journal, Vol. 83 no. 3, pp. 1595–1612, 2002.
 [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, M. Stahl, A medicinal chemist’s guide to molecular interactions, Journal of Medicinal Chemistry Vol. 53 no. 14, pp. 5061–5084, 2010
 [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

Miscellaneous

 [Aalten-1996] D.M.F. van Aalten, R. Bywater, J.B.C. Findlay, M. Hendlich, R.W.W. Hooft and G. Vriend, PRODRG: A Program for Generating Molecular Topologies and Unique Molecular Descriptors from Coordinates of Small Molecules, Journal of Computer-Aided Molecular Design, Vol. 10, pp. 255–262, 1996.
 [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,
 [Bondi-1964] A. Bondi, van der Waals Volumes and Radii, Journal of Physical Chemistry, Vol. 68, pp. 441-451, 1964
 [Dalby-1992] A. Dalby, J.G. Nourse, W.D. Hounshell, Aki Gushurst, D.L. Grier, B.A. Leland and J. Laufer, Description of Several Chemical-Structure File Formats Used by Computer-Programs developed at Molecular Design Limited, Journal of Chemical Information and Computer Science, Vol. 32, pp. 244–255, 1992.
 [Nicholls-2008] Anthony Nicholls, David L. Mobley, J. Peter Guthrie, John D. Chodera, Christopher I. Bayly, Matthew D. Cooper and Vijay S. Pande, Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry Journal of Medicinal Chemistry Vol. 51, pp 769–779, 2008.
 [Nicholls-2010] Anthony Nicholls, Stanislaw Wlodek and J. Andrew Grant, SAMPL2 and continuum modeling Journal of Computer-Aided Molecular Design, Vol. 24, pp 293–306, 2010.
 [Pauling-1960] Linus Pauling, The Nature of the Chemical Bond and the Structure of Molecules and Crystals; An Introduction to Modern Structural Chemistry, Cornell University Press; 3 edition (1960), ISBN-13: 978-0801403330
 [Rashin-1985] Alexander A. Rashin, Barry Honig, Reevaluation of the Born model of ion hydration, Journal of Physical Chemistry, Vol. 89, pp. 5588–5593, 1985.
 [Sutton-1958] L.E.Sutton Tables of Interatomic Distances and Configuration in Molecules and Ions, Chem. Soc., London Special Publication, No.11, 1958
 [Walters-1996] W.P. Walters and S.H. Yalkowsky, ESCHER - A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology, Journal of Chemical Information and Computer Science, Vol. 36, pp. 1015–1017, 1996.
 [Kabsch-1983] W. Kabsch and C. Sander, Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features, Biopolymers, Vol. 22, pp. 2577–2637, 1983.
 [Theobald-2005] D.L. Theobald Rapid calculation of RMSDs using a quaternion-based characteristic polynomial, Acta Crystallogr A, Vol. 51, pp. 478–480, 2005.
 [Liu-2010] P. Liu, D.K. Agrafiotis, and D.L. Theobald Fast determination of the optimal rotation matrix for macromolecular superpositions, Computational Chemistry, Vol. 31, pp. 1561–1563, 2010.
 [Kelly-1965] K. Kelly, Twenty-Two Colors of Maximum Contrast, Color Eng., Vol. 3, No. 6, pp. 26–27 1965
 [Green-Armytage-2010] P. Green-Armytage, A Color Alphabet and the Limit of Color Coding, Colors: Design & Creativity., Vol. 6, No. 10, pp. 1–23 2010