Why do we need so many chemical similarity search methods?

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196

Chemical Similarity Searching

Willett, P., Barnard, J. M., & Downs, G. M. (1998) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci9800211 · Cited by 1,775

Concepts and applications of molecular similarity

Johnson, M. A., & Maggiora, G. M. (1990) · Wiley eBooks · Cited by 1,301

Atom pairs as molecular features in structure-activity studies: definition and applications

Carhart, R. E., Smith, D. H., & Venkataraghavan, R. (1985) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci00046a002 · Cited by 1,101

Virtual screening—an overview

Walters, W. P., Stahl, M. T., & Murcko, M. A. (1998) · Drug Discovery Today · doi:10.1016/s1359-6446(97)01163-x · Cited by 996

Consensus scoring: a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.

Charifson, P. S., Corkery, J. J., Murcko, M. A., & Walters, W. P. (1999) · Journal of Medicinal Chemistry · doi:10.1021/jm990352k · Cited by 698

Use of Structure−Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection

Brown, R. D., & Martin, Y. C. (1996) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci9501047 · Cited by 631

Neighborhood Behavior: A Useful Concept for Validation of “Molecular Diversity” Descriptors

Patterson, D. E., CRAMER, R. D. I., Ferguson, A. M., Clark, R. D., & Weinberger, L. E. (1996) · Journal of Medicinal Chemistry · doi:10.1021/jm960290n · Cited by 509

The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding

Brown, R. D., & Martin, Y. C. (1997) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci960373c · Cited by 378

New 4-Point Pharmacophore Method for Molecular Similarity and Diversity Applications: Overview of the Method and Applications, Including a Novel Approach to the Design of Combinatorial Libraries Containing Privileged Substructures

Mason, J. S., Morize, I., Menard, P. R., Cheney, D. L., Hulme, C., & Labaudinière, R. F. (1999) · Journal of Medicinal Chemistry · doi:10.1021/jm9806998 · Cited by 375

Topological torsion: a new molecular descriptor for SAR applications. Comparison with other descriptors

Nilakantan, R., Bauman, N., Dixon, J. S., & Venkataraghavan, R. (1987) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci00054a008 · Cited by 367

The Coding of the Three-Dimensional Structure of Molecules by Molecular Transforms and Its Application to Structure-Spectra Correlations and Studies of Biological Activity

Schuur, J., Selzer, P. M., & Gasteiger, J. (1996) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci950164c · Cited by 351

On the Properties of Bit String-Based Measures of Chemical Similarity

Flower, D. R. (1998) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci970437z · Cited by 347

Feature trees: A new molecular similarity measure based on tree matching

Rarey, M., & Dixon, J. S. (1998) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1008068904628 · Cited by 329

An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap

Kearsley, S. K., & SMITH, G. M. (1990) · Tetrahedron Computer Methodology · doi:10.1016/0898-5529(90)90162-2 · Cited by 313

FLOG: A system to select ?quasi-flexible? ligands complementary to a receptor of known three-dimensional structure

Miller, M. D., Kearsley, S. K., Underwood, D. J., & Sheridan, R. P. (1994) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf00119865 · Cited by 281

Chemical Similarity Using Physiochemical Property Descriptors

Kearsley, S. K., Sallamack, S. J., Fluder, E. M., Andose, J. D., Mosley, R. T., & Sheridan, R. P. (1996) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci950274j · Cited by 267

Metric Validation and the Receptor-Relevant Subspace Concept

Pearlman, R. S., & Smith, K. M. (1999) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci980137x · Cited by 264

Computational methods for the structural alignment of molecules

Lemmen, C., & Lengauer, T. (2000) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1008194019144 · Cited by 262

The Characterization of Chemical Structures Using Molecular Properties. A Survey

Livingstone, D. J. (1999) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci990162i · Cited by 250

Selected Concepts and Investigations in Compound Classification, Molecular Descriptor Analysis, and Virtual Screening

Bajorath, J. (2001) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci0001482 · Cited by 227

A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization

Liwo, A., Pincus, M. R., Wawak, R. J., Rackovsky, S. R., dziej, S. O., & Scheraga, H. A. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199705)18:7 · Cited by 186

Clustering of Large Databases of Compounds: Using the MDL “Keys” as Structural Descriptors

McGregor, M. J., & Pallai, P. V. (1997) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci960151e · Cited by 181

Stigmata: An Algorithm To Determine Structural Commonalities in Diverse Datasets

Shemetulskis, N. E., Weininger, D., Blankley, C. J., Yang, J. J., & Humblet, C. C. (1996) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci950169+ · Cited by 159

Diversity Profiling and Design Using 3D Pharmacophores: Pharmacophore-Derived Queries (PDQ)

Pickett, S. D., Mason, J. S., & McLay, I. M. (1996) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci960039g · Cited by 154

Protocols for Bridging the Peptide to Nonpeptide Gap in Topological Similarity Searches

Sheridan, R. P., Singh, S. B., Fluder, E. M., & Kearsley, S. K. (2001) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci0100144 · Cited by 140

Comparing 3D Pharmacophore Triplets and 2D Fingerprints for Selecting Diverse Compound Subsets

Matter, H., & Pötter, T. (1999) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci980185h · Cited by 117

Flexibases: A way to enhance the use of molecular docking methods

Kearsley, S. K., Underwood, D. J., Sheridan, R. P., & Miller, M. D. (1994) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf00123666 · Cited by 117

Morphological similarity: A 3D molecular similarity method correlated with protein-ligand recognition

Jain, A. N. (2000) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1008100132405 · Cited by 116

Molecular substructure similarity searching: efficient retrieval in two-dimensional structure databases

Hagadone, T. R. (1992) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci00009a019 · Cited by 109

SQ: A Program for Rapidly Producing Pharmacophorically Relevent Molecular Superpositions

Miller, M. D., Sheridan, R. P., & Kearsley, S. K. (1999) · Journal of Medicinal Chemistry · doi:10.1021/jm9806143 · Cited by 107

Chemical database techniques in drug discovery

Miller, M. A. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd745 · Cited by 101

One-Dimensional Molecular Representations and Similarity Calculations: Methodology and Validation

Dixon, S. L., & Merz, K. M. (2001) · Journal of Medicinal Chemistry · doi:10.1021/jm010137f · Cited by 100

Similarity Searching in Files of Three-Dimensional Chemical Structures: Analysis of the BIOSTER Database Using Two-Dimensional Fingerprints and Molecular Field Descriptors

Schuffenhauer, A., Gillet, V. J., & Willett, P. (1999) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci990263g · Cited by 85

Large-scale virtual screening for discovering leads in the postgenomic era

Waszkowycz, B., Perkins, T. D. J., Sykes, R. A., & Li, J. (2001) · IBM Systems Journal · doi:10.1147/sj.402.0360 · Cited by 84

Toward General Methods of Targeted Library Design: Topomer Shape Similarity Searching with Diverse Structures as Queries

Andrews, K. M., & CRAMER, R. D. I. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm000003m · Cited by 78

Similarity Searching in Files of Three-Dimensional Chemical Structures. Alignment of Molecular Electrostatic Potential Fields with a Genetic Algorithm

Wild, D. J., & Willett, P. (1996) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci9500851 · Cited by 75

Combination of molecular similarity measures using data fusion

Ginn, C. M. R., Willett, P., & Bradshaw, J. (2005) · Kluwer Academic Publishers eBooks · doi:10.1007/0-306-46883-2_1 · Cited by 70

Effectiveness of retrieval in similarity searches of chemical databases: a review of performance measures

Edgar, S. J., Holliday, J. D., & Willett, P. (2000) · Journal of Molecular Graphics and Modelling · doi:10.1016/s1093-3263(00)00061-9 · Cited by 68

Extending the trend vector: The trend matrix and sample-based partial least squares

Sheridan, R. P., Nachbar, R. B., & Bush, B. L. (1994) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf00126749 · Cited by 62

PATTY: A programmable atom type and language for automatic classification of atoms in molecular databases

Bush, B. L., & Sheridan, R. P. (1993) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci00015a015 · Cited by 61

Molecular Hologram QSAR

Heritage, T. W., & Lowis, D. R. (1999) · ACS symposium series · doi:10.1021/bk-1999-0719.ch014 · Cited by 57

IcePick: A Flexible Surface-Based System for Molecular Diversity

Mount, J., Ruppert, J., Welch, W., & Jain, A. N. (1998) · Journal of Medicinal Chemistry · doi:10.1021/jm970775r · Cited by 55

Molecular Descriptors for Effective Classification of Biologically Active Compounds Based on Principal Component Analysis Identified by a Genetic Algorithm

Xue, L., & Bajorath, J. (2000) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci000322m · Cited by 54

Design and Diversity Analysis of Large Combinatorial Libraries Using Cell-Based Methods

Schnur, D. M. (1999) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci980138p · Cited by 51

Fingerprint Scaling Increases the Probability of Identifying Molecules with Similar Activity in Virtual Screening Calculations

Xue, L., Stahura, F. L., Godden, J. W., & Bajorath, J. (2001) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci000311t · Cited by 50

Computation of the physio‐chemical properties and data mining of large molecular collections

Cheng, A., Diller, D., Dixon, S. L., Egan, W. J., Lauri, G., & Merz, K. M. (2001) · Journal of Computational Chemistry · doi:10.1002/jcc.1164 · Cited by 50

Comparison of Knowledge-Based and Distance Geometry Approaches for Generation of Molecular Conformations

Feuston, B. P., Miller, M. D., Culberson, J. C., Nachbar, R. B., & Kearsley, S. K. (2001) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci000464g · Cited by 50

Measuring Molecular Similarity and Diversity: Total Pharmacophore Diversity

Makara, G. M. (2001) · Journal of Medicinal Chemistry · doi:10.1021/jm010036h · Cited by 48

Chemistry Space Metrics in Diversity Analysis, Library Design, and Compound Selection

Menard, P. R., Mason, J. S., Morize, I., & Bauerschmidt, S. (1998) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci9801062 · Cited by 44

Database searching on the basis of three-dimensional molecular similarity using the SPERM program

Perry, N. C., & van Geerestein, V. J. (1992) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci00010a006 · Cited by 43

Latent Semantic Structure Indexing (LaSSI) for Defining Chemical Similarity

Hull, R., Singh, S. B., Nachbar, R. B., Sheridan, R. P., Kearsley, S. K., & Fluder, E. M. (2001) · Journal of Medicinal Chemistry · doi:10.1021/jm000393c · Cited by 32

The Centroid Approximation for Mixtures: Calculating Similarity and Deriving Structure−Activity Relationships

Sheridan, R. P. (2000) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci000045j · Cited by 30

Chemical Similarity Searches Using Latent Semantic Structural Indexing (LaSSI) and Comparison to TOPOSIM

Hull, R., Fluder, E. M., Singh, S. B., Nachbar, R. B., Kearsley, S. K., & Sheridan, R. P. (2001) · Journal of Medicinal Chemistry · doi:10.1021/jm000392k · Cited by 21

Mining the Chemical Quarry with Joint Chemical Probes: An Application of Latent Semantic Structure Indexing (LaSSI) and TOPOSIM (Dice) to Chemical Database Mining

Singh, S. B., Sheridan, R. P., Fluder, E. M., & Hull, R. (2001) · Journal of Medicinal Chemistry · doi:10.1021/jm000398+ · Cited by 15

ChemInform Abstract: PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases.

Bush, B. L., & Sheridan, R. P. (1994) · ChemInform · doi:10.1002/chin.199402294 · Cited by 13

Relating protein pharmacology by ligand chemistry

Keiser, M. J., Roth, B. L., Armbruster, B. N., Ernsberger, P., Irwin, J. J., & Shoichet, B. K. (2007) · Nature Biotechnology · doi:10.1038/nbt1284 · Cited by 2,402

Machine learning in chemoinformatics and drug discovery

Lo, Y.-C., Rensi, S. E., Torng, W., & Altman, R. B. (2018) · Drug Discovery Today · doi:10.1016/j.drudis.2018.05.010 · Cited by 960

Integration of virtual and high-throughput screening

Bajorath, J. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd941 · Cited by 935

QSAR without borders

Muratov, E. N., Bajorath, J., Sheridan, R. P., Tetko, I. V., Filimonov, D., Poroikov, V., Oprea, T. I., Baskin, I. I., Varnek, A., Roitberg, A., et al. (2020) · Chemical Society Reviews · doi:10.1039/d0cs00098a · Cited by 913

Similarity-based virtual screening using 2D fingerprints

Willett, P. (2006) · Drug Discovery Today · doi:10.1016/j.drudis.2006.10.005 · Cited by 849

Similarity searching

Stumpfe, D., & Bajorath, J. (2011) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.23 · Cited by 126

Applications of Information Retrieval Methods in Computer-Aided Drug Discovery

Willett, P. (2001) · White Rose Research Online (University of Leeds, The University of Sheffield, University of York) · Cited by 1

Comparison of Similarity Method to Improve Retrieval Performance for Chemical Data

Nurjana, N. R., & Zainudin, S. (2018) · Asia-Pacific Journal of Information Technology and Multimedia · doi:10.17576/apjitm-2018-0701-08 · Cited by 2

Chemical similarity searches: when is complexity justified?

Sheridan, R. P. (2007) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2.4.423 · Cited by 49

Large-Scale Comparison of Alternative Similarity Search Strategies with Varying Chemical Information Contents

Laufkötter, O., Miyao, T., & Bajorath, J. (2019) · ACS Omega · doi:10.1021/acsomega.9b02470 · Cited by 10