Ring Perception

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.
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.
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.
John Figueras,
Ring Perception Using Breadth-First Search,
Journal of Chemical Information and Computer Science, Vol. 36, pp. 986–991, 1996.
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.
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.
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.
M. J. Plotkin,
Mathematical Basis of Ring-Finding Algorithms in CIDS,
Journal of Chemical Documentation, Vol. 11, pp. 60–63, 1971.
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.
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.
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.
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

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

Connectivity Perception

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.
Simon K. Kearsley,
A Quick Robust Method for Assigning A Kekulé Structure,
Computers in Chemistry, Vol. 17, pp. 1–10, 1993.
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.
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.

Substructure Search

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

Molecule Canonicalization


Maximum Common Substructure Search

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
James J. McGregor,
Backtrack Search Algorithms and the Maximal Common Subgraph Problem,
Software – Practice and Experience, Vol. 12, pp. 23–34, 1982.
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
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

Johann Gasteiger and M. Marsili,
A New Model for Calculating Atomic Charges in Molecules,
Tetrahedron Letters, pp. 3181–3184, 1978.
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

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

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.
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.
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.

Molecular Line Notation

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.
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.

Rotamer Libraries

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.
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.
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

G.N. Ramachandran, C. Ramakrishnan, V. Sasisekharan,
Stereochemistry of polypeptide chain configurations.
Journal of Molecular Biology, Vol. 7, pp. 95–99, 1963.
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.
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 \(C\alpha\) geometry \(\phi\), \(\psi\) and \(C\beta\) deviation.
Proteins, Vol. 50 pp. 437–450, 2003.

Biomolecular Structure Quality Assessment

D. M. Blow,
Rearrangement of Cruickshank’s formulae for the diffraction-component precision index,
Acta Crystallogr D 58, pp. 792-7, 2002.
D. W. J. Cruickshank,
Remarks about protein structure precision,
Acta Crystallogr D 55, pp. 583-601, 1999.
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 Crystallogr D 66, pp. 12-21, 2010.
Greg L. Warren, Thanh D. Do, Brian P. Kelley, Anthony Nicholls and Stephen D. Warren,
Essential considerations for using protein–ligand structures in drug discovery,
Drug Discovery Today, Vol. 17, pp. 1270–1281, 2012.

Protein Loop Modeling

Karen A. Rossi, Carolyn A. Weigelt, Akbar Nayeem and Stanley R. Krystek Jr.,
Loopholes and missing links in protein modeling,
Protein Science, Vol. 16, pp. 1999–2012, 2007.

Sequence Alignment

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.
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.
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

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.
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, M. Stahl,
A medicinal chemist’s guide to molecular interactions,
Journal of Medicinal Chemistry Vol. 53 no. 14, pp. 5061–5084, 2010
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,
A. Bondi,
van der Waals Volumes and Radii,
Journal of Physical Chemistry, Vol. 68, pp. 441-451, 1964
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.
Anthony Nicholls, Stanislaw Wlodek and J. Andrew Grant,
SAMPL2 and continuum modeling
Journal of Computer-Aided Molecular Design, Vol. 24, pp 293–306, 2010.
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
Alexander A. Rashin, Barry Honig,
Reevaluation of the Born model of ion hydration,
Journal of Physical Chemistry, Vol. 89, pp. 5588–5593, 1985.
Tables of Interatomic Distances and Configuration in Molecules and Ions,
Chem. Soc., London Special Publication, No.11, 1958
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.
K. Kelly,
Twenty-Two Colors of Maximum Contrast,
Color Eng., Vol. 3, No. 6, pp. 26–27 1965
P. Green-Armytage,
A Color Alphabet and the Limit of Color Coding,
Colors: Design & Creativity., Vol. 6, No. 10, pp. 1–23 2010
F. J. Gamo, L. M. Sanz, J. Vidal, C. de Cozar, E. Alvarez, J. L. Lavandera, D. E. Vanderwall,
D. V. S. Green, V. Kumar, S. Hasan, J. R. Brown, C. E. Peishoff, L. R. Cardon, J. F. Garcia-Bustos.
Thousands of chemical starting points for antimalarial lead identification, Nature, Vol. 465, pp. 305–310, 2010
N. Friedrich, A. Meyder, C. de Bruyn Kops, K. Sommer, F. Flachsenberg, M. Rarey and J. Kirchmair.
High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators,
|JCIM|, Vol. 57, No. 3, pp. 529-539 2017
P. C. D. Hawkins, S. J. Wlodek, Decisions With Confidence: Application to the Conformation Sampling of Molecules in the Solid-State,
|JCIM|, 2020, submitted