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Ring Perception

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Efficient Exact Solution of the Ring Perception Problem,

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Baumer-1991

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Down-1989

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Figueras-1996

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Ring Perception Using Breadth-First Search,

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Fujita-1988

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A new algorithm for selection of synthetically important rings. The essential set of essential rings for organic structures,

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Gasteiger-1979

Johann Gasteiger and Clemens Jochum,

An Algorithm for the Perception of Synthetically Important Rings,

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Hanser-1996

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Plotkin-1971

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Qian-1990

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Roos-Kozel-1981

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Takahashi-1994

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Automatic extraction of ring substructures from a chemical structure,

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Zamora-1979

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An Algorithm for Finding the Smallest Set of Smallest Rings,

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Aromaticity Perception

Lloyd-1996

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Connectivity Perception

Baber-1992

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Automatic Assignment of Chemical Connectivity to Organic Molecules in the Cambridge Structural Database,

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Kearsley-1993

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A Quick Robust Method for Assigning A Kekulé Structure,

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Meng-1991

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Determination of Molecular Topology and Atomic Hybridization States from Heavy Atom Coordinates,

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Rippmann-1997

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Substructure Search

Figueras-1972

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Substructure search by set reduction.

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Ullman-1976

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Molecule Canonicalization

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Maximum Common Substructure Search

Bunke-2002

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A Comparison of Algorithms for Maximum Common Subgraph on Randomly Connected Graphs,

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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,

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Raymond-2002

W. R. Raymond, E.J. Gardiner, and P. Willett,

Rascal: Calculation of Graph Similarity Using Maximum Common Edge Subgraphs,

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Wang-1997

T. Wang, and J. Zhou,

EMCSS: A New Method for Maximum Common Substructure Search,

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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,

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Atom Type Assignment

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,

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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,

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Vidal-2005

David Vidal, Michael Thormann, and Miquel Pons,

LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities

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Vidal-2006

David Vidal, Michael Thormann, and Miquel Pons,

A Novel Search Engine for Virtual Screening of Very Large Databases,

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Molecular Line Notation

Weininger-1988

David Weininger,

SMILES: A Chemical Language and Information System: 1. Introduction to Methodology and Encoding Rules,

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Weininger-1989

David Weininger, Arthur Weininger and Joseph L. Weininger,

SMILES 2: Algorithm for Generation of Unique SMILES Notation,

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Rotamer Libraries

Dunbrack-1997

R.L. Dunbrack, Jr., F.E. Cohen,

Bayesian statistical analysis of protein side-chain rotamer preferences,

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Lovell-2000

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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.

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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 \(C\alpha\) geometry \(\phi\), \(\psi\) and \(C\beta\) deviation.

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Biomolecular Structure Quality Assessment

Blow-2002

D. M. Blow,

Rearrangement of Cruickshank’s formulae for the diffraction-component precision index,

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Cruickshank-1999

D. W. J. Cruickshank,

Remarks about protein structure precision,

Acta Crystallogr D 55, pp. 583-601, 1999.

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.

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Warren-2012

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,

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Protein Loop Modeling

Rossi-2007

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.

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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.

(online: http://www.cell.com/biophysj/abstract/S0006-3495(02)73929-5)

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, 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)

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)

Miscellaneous

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)

Bondi-1964

A. Bondi,

van der Waals Volumes and Radii,

Journal of Physical Chemistry, Vol. 68, pp. 441-451, 1964

(online: http://pubs.acs.org/doi/abs/10.1021/j100785a001)

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,

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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.

(online: http://pubs.acs.org/doi/abs/10.1021/j100272a006)

Sutton-1958

L.E.Sutton

Tables of Interatomic Distances and Configuration in Molecules and Ions,

Chem. Soc., London Special Publication, No.11, 1958

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.

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

Gamo-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

Friedrich-2017

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

Hawkins-2020

P. C. D. Hawkins, S. J. Wlodek, Decisions With Confidence: Application to the Conformation Sampling of Molecules in the Solid-State,

|JCIM|, 2020, submitted