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 · see citing works

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 · see citing works

Concepts and applications of molecular similarity

Johnson, M. A., & Maggiora, G. M. (1990) · Wiley eBooks · Cited by 1,322 · see citing works

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 1,120 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 379 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 345 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 253 · see citing works

A united‐residue force field for off‐lattice protein‐structure simulations. I. Functional forms and parameters of long‐range side‐chain interaction potentials from protein crystal data

Liwo, A., Ołdziej, S., Pincus, M. R., Wawak, R., Rackovsky, S., & Scheraga, H. A. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199705)18:7 · Cited by 239 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Chemical database techniques in drug discovery

Miller, M. A. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd745 · Cited by 100 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Molecular Hologram QSAR

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

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Measuring Molecular Similarity and Diversity: Total Pharmacophore Diversity

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

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Integration of virtual and high-throughput screening

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

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 · see citing works

Similarity-based virtual screening using 2D fingerprints

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

Virtual Screening Workflow Development Guided by the “Receiver Operating Characteristic” Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4

Triballeau, N., Acher, F., Brabet, I., Pin, J., & Bertrand, H. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm049092j · Cited by 633 · see citing works

Computer-Aided Drug Design Methods

Yu, W., & MacKerell, A. D. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6634-9_5 · Cited by 599 · see citing works

SuperPred: update on drug classification and target prediction

Nickel, J., Gohlke, B.-O., Erehman, J., Banerjee, P., Rong, W. W., Goede, A., Dunkel, M., & Preißner, R. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku477 · Cited by 590 · see citing works

Charting biologically relevant chemical space: A structural classification of natural products (SCONP)

Koch, М. A., Schuffenhauer, A., Scheck, M., Wetzel, S., Casaulta, M., Odermatt, A., Ertl, P., & Waldmann, H. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503647102 · Cited by 544 · see citing works

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

Rifaioğlu, A. S., Ataş, H., Martin, M. J., Çetin-Atalay, R., Atalay, V., & Doğan, T. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby061 · Cited by 535 · see citing works

Machine learning methods in chemoinformatics

Mitchell, J. B. O. (2014) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1183 · Cited by 470 · see citing works

Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches

Geppert, H., & Bajorath, J. (2007) · Drug Discovery Today · doi:10.1016/j.drudis.2007.01.011 · Cited by 466 · see citing works

Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods

Duan, J., Dixon, S. L., Lowrie, J. F., & Sherman, W. (2010) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2010.05.008 · Cited by 445 · see citing works

ZINCPharmer: pharmacophore search of the ZINC database

Koes, D. R., & Camacho, C. J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks378 · Cited by 436 · see citing works

Comparison of Topological, Shape, and Docking Methods in Virtual Screening

McGaughey, G. B., Sheridan, R. P., Bayly, C. I., Culberson, J. C., Kreatsoulas, C., Lindsley, S. R., Maiorov, V. N., Truchon, J., & Cornell, W. D. (2007) · Journal of Chemical Information and Modeling · doi:10.1021/ci700052x · Cited by 418 · see citing works

Designing screens: how to make your hits a hit

Walters, W. P., & Namchuk, M. (2003) · Nature Reviews Drug Discovery · doi:10.1038/nrd1063 · Cited by 377 · see citing works

Identification of chemically diverse Chk1 inhibitors by receptor-based virtual screening

Foloppe, N., Fisher, L. M., Howes, R., Potter, A. J., Robertson, A., & Surgenor, A. E. (2006) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2006.03.021 · Cited by 363 · see citing works

Open-source platform to benchmark fingerprints for ligand-based virtual screening

Riniker, S., & Landrum, G. A. (2013) · Journal of Cheminformatics · doi:10.1186/1758-2946-5-26 · Cited by 363 · see citing works

The 7 TM G‐Protein‐Coupled Receptor Target Family

Jacoby, E., Bouhelal, R., Gerspacher, M., & Seuwen, K. (2006) · ChemMedChem · doi:10.1002/cmdc.200600134 · Cited by 357 · see citing works

Scaffold hopping

Böhm, H., Flohr, A., & Ståhl, M. (2004) · Drug Discovery Today Technologies · doi:10.1016/j.ddtec.2004.10.009 · Cited by 337 · see citing works

Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures

Hert, J., Willett, P., Wilton, D. J., Acklin, P., Azzaoui, K., Jacoby, E., & Schuffenhauer, A. (2004) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci034231b · Cited by 310 · see citing works

An overview of molecular fingerprint similarity search in virtual screening

Muegge, I., & Mukherjee, P. K. (2015) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2016.1117070 · Cited by 278 · see citing works

Chemogenomic approaches to rational drug design

Rognan, D. (2007) · British Journal of Pharmacology · doi:10.1038/sj.bjp.0707307 · Cited by 265 · see citing works

Active-learning strategies in computer-assisted drug discovery

Reker, D., & Schneider, G. (2014) · Drug Discovery Today · doi:10.1016/j.drudis.2014.12.004 · Cited by 262 · see citing works

Virtual Screening of Molecular Databases Using a Support Vector Machine

Jorissen, R. N., & Gilson, M. K. (2005) · Journal of Chemical Information and Modeling · doi:10.1021/ci049641u · Cited by 258 · see citing works

Deep Reinforcement Learning for Multiparameter Optimization in de novo Drug Design

Ståhl, N., Falkman, G., Karlsson, A., Mathiason, G., & Boström, J. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00325 · Cited by 239 · see citing works

Learning Molecular Representations for Medicinal Chemistry

Chuang, K. V., Gunsalus, L. M., & Keiser, M. J. (2020) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c00385 · Cited by 227 · see citing works

A maximum common substructure-based algorithm for searching and predicting drug-like compounds

Cao, Y., Jiang, T., & Girke, T. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn186 · Cited by 211 · see citing works

ChemGPS-NP: Tuned for Navigation in Biologically Relevant Chemical Space

Larsson, J., Gottfries, J., Mureşan, S., & Backlund, A. (2007) · Journal of Natural Products · doi:10.1021/np070002y · Cited by 209 · see citing works

Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery

Kumar, A., & Zhang, K. Y. J. (2018) · Frontiers in Chemistry · doi:10.3389/fchem.2018.00315 · Cited by 201 · see citing works

Bridging Chemical and Biological Space: “Target Fishing” Using 2D and 3D Molecular Descriptors

Nettles, J. H., Jenkins, J. L., Bender, A., Deng, Z., Davies, J. W., & Glick, M. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm060902w · Cited by 202 · see citing works

New Methods for Ligand-Based Virtual Screening: Use of Data Fusion and Machine Learning to Enhance the Effectiveness of Similarity Searching

Hert, J., Willett, P., Wilton, D. J., Acklin, P., Azzaoui, K., Jacoby, E., & Schuffenhauer, A. (2006) · Journal of Chemical Information and Modeling · doi:10.1021/ci050348j · Cited by 202 · see citing works

Activity cliffs in drug discovery: Dr Jekyll or Mr Hyde?

Cruz‐Monteagudo, M., Medina‐Franco, J. L., Pérez‐Castillo, Y., Nicolotti, O., Cordeiro, M. N. D. S., & Borges, F. (2014) · Drug Discovery Today · doi:10.1016/j.drudis.2014.02.003 · Cited by 193 · see citing works

ErG: 2D Pharmacophore Descriptions for Scaffold Hopping

Stiefl, N., Watson, I. A., Baumann, K., & Zaliani, A. (2005) · Journal of Chemical Information and Modeling · doi:10.1021/ci050457y · Cited by 191 · see citing works

Scaffold Hopping through Virtual Screening Using 2D and 3D Similarity Descriptors: Ranking, Voting, and Consensus Scoring

Zhang, Q., & Muegge, I. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm050468i · Cited by 183 · see citing works

The many roles of molecular complexity in drug discovery

Méndez-Lucio, O., & Medina-Franco, J. L. (2017) · Drug Discovery Today · doi:10.1016/j.drudis.2016.08.009 · Cited by 180 · see citing works

SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 1. Method and Assessment of Virtual Screening

Liu, X., Jiang, H., & Li, H. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200060s · Cited by 173 · see citing works

Pharmer: Efficient and Exact Pharmacophore Search

Koes, D. R., & Camacho, C. J. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200097m · Cited by 172 · see citing works

Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs

Medina‐Franco, J. L., Martínez‐Mayorga, K., Bender, A., Marín, R. M., Giulianotti, M. A., Pinilla, C., & Houghten, R. A. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci800379q · Cited by 152 · see citing works

Searching Techniques for Databases of Two- and Three-Dimensional Chemical Structures

Willett, P. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm0582165 · Cited by 151 · see citing works

Combination of Similarity Rankings Using Data Fusion

Willett, P. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci300547g · Cited by 150 · see citing works

Similarity Searching Using Reduced Graphs

Gillet, V. J., Willett, P., & Bradshaw, J. (2003) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci025592e · Cited by 150 · see citing works

Metrics for measuring distances in configuration spaces

Sadeghi, A., Ghasemi, S. A., Schaefer, B., Mohr, S., Lill, M. A., & Goedecker, S. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4828704 · Cited by 141 · see citing works

Strategies for 3D pharmacophore-based virtual screening

Seidel, T., Ibis, G., Bendix, F., & Wolber, G. (2010) · Drug Discovery Today Technologies · doi:10.1016/j.ddtec.2010.11.004 · Cited by 137 · see citing works

Molecular Similarity Measures

Maggiora, G. M., & Shanmugasundaram, V. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-839-3_2 · Cited by 134 · see citing works

Advances in virtual screening

Muegge, I., & Oloff, S. (2006) · Drug Discovery Today Technologies · doi:10.1016/j.ddtec.2006.12.002 · Cited by 134 · see citing works

Similarity Searching Using 2D Structural Fingerprints

Willett, P. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-839-3_5 · Cited by 133 · see citing works

A Simple Representation of Three-Dimensional Molecular Structure

Axen, S. D., Huang, X., Cáceres, E. L., Gendelev, L., Roth, B. L., & Keiser, M. J. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b00696 · Cited by 133 · see citing works

The Calculation of Molecular Structural Similarity: Principles and Practice

Willett, P. (2014) · Molecular Informatics · doi:10.1002/minf.201400024 · Cited by 131 · see citing works

A 3D Similarity Method for Scaffold Hopping from Known Drugs or Natural Ligands to New Chemotypes

Jenkins, J. L., Glick, M., & Davies, J. W. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm049654z · Cited by 130 · see citing works

Small Molecule Subgraph Detector (SMSD) toolkit

Rahman, S. A., Bashton, M., Holliday, G. L., Schrader, R., & Thornton, J. M. (2009) · Journal of Cheminformatics · doi:10.1186/1758-2946-1-12 · Cited by 127 · see citing works

Comparison of Structure‐ and Ligand‐Based Virtual Screening Protocols Considering Hit List Complementarity and Enrichment Factors

Krüger, D. M., & Evers, A. (2009) · ChemMedChem · doi:10.1002/cmdc.200900314 · Cited by 126 · see citing works

Quantitative structure–activity relationship: promising advances in drug discovery platforms

Wang, T., Wu, M., Lin, J., & Yang, L.-R. (2015) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2015.1083006 · Cited by 124 · see citing works

Evaluation of machine-learning methods for ligand-based virtual screening

Chen, B., Harrison, R. F., Papadatos, G., Willett, P., Wood, D., Lewell, X. Q., Greenidge, P. A., & Stiefl, N. (2007) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-006-9096-5 · Cited by 124 · see citing works

Similarity searching

Stumpfe, D., & Bajorath, J. (2011) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.23 · Cited by 124 · see citing works

Tautomerism in Computer‐Aided Drug Design

Pospíšil, P., Ballmer, P., Scapozza, L., & Folkers, G. (2003) · Journal of Receptors and Signal Transduction · doi:10.1081/rrs-120026975 · Cited by 122 · see citing works

Advances and applications of machine learning and deep learning in environmental ecology and health

Cui, S., Gao, Y., Huang, Y., Shen, L., Zhao, Q., Pan, Y., & Zhuang, S. (2023) · Environmental Pollution · doi:10.1016/j.envpol.2023.122358 · Cited by 124 · see citing works

Pharmacophore Modeling, Quantitative Structure–Activity Relationship Analysis, and in Silico Screening Reveal Potent Glycogen Synthase Kinase-3β Inhibitory Activities for Cimetidine, Hydroxychloroquine, and Gemifloxacin

Taha, M. O., Bustanji, Y. K., Al-Ghussein, M. A. S., Mohammad, M., Zalloum, H. M., Almasri, I. M., & Atallah, N. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm7009765 · Cited by 109 · see citing works

A ‘rule of 0.5’ for the metabolite-likeness of approved pharmaceutical drugs

O’Hagan, S., Swainston, N., Handl, J., & Kell, D. B. (2014) · Metabolomics · doi:10.1007/s11306-014-0733-z · Cited by 101 · see citing works

Ligand-Target Prediction Using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics

Nigsch, F., Bender, A., Jenkins, J. L., & Mitchell, J. B. O. (2008) · Journal of Chemical Information and Modeling · doi:10.1021/ci800079x · Cited by 102 · see citing works

Similarity methods in chemoinformatics

Willett, P. (2009) · Annual Review of Information Science and Technology · doi:10.1002/aris.2009.1440430108 · Cited by 99 · see citing works

Optimal assignment methods for ligand-based virtual screening

Jahn, A., Hinselmann, G., Fechner, N., & Zell, A. (2009) · Journal of Cheminformatics · doi:10.1186/1758-2946-1-14 · Cited by 94 · see citing works

The Pharmacophore Concept and Its Applications in Computer-Aided Drug Design

Seidel, T., Schuetz, D. A., Garon, A., & Langer, T. (2019) · Fortschritte der Chemie Organischer Naturstoffe/Fortschritte der Chemie organischer Naturstoffe/Progress in the chemistry of organic natural products · doi:10.1007/978-3-030-14632-0_4 · Cited by 90 · see citing works

Scaffold Hopping Using Two-Dimensional Fingerprints: True Potential, Black Magic, or a Hopeless Endeavor? Guidelines for Virtual Screening

Vogt, M., Stumpfe, D., Geppert, H., & Bajorath, J. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm100492z · Cited by 89 · see citing works

Scaffold Hopping Using Clique Detection Applied to Reduced Graphs

Barker, E. J., Buttar, D., Cosgrove, D. A., Gardiner, E. J., Kitts, P., Willett, P., & Gillet, V. J. (2006) · Journal of Chemical Information and Modeling · doi:10.1021/ci050347r · Cited by 89 · see citing works

Chemical Multiverse: An Expanded View of Chemical Space

Medina‐Franco, J. L., Chávez‐Hernández, A. L., López‐López, E., & Saldívar‐González, F. I. (2022) · Molecular Informatics · doi:10.1002/minf.202200116 · Cited by 86 · see citing works

Probabilistic Approaches in Activity Prediction

Filimonov, D. A., & Poroikov, V. (2008) · Royal Society of Chemistry eBooks · doi:10.1039/9781847558879-00182 · Cited by 90 · see citing works

Discovery of new potent human protein tyrosine phosphatase inhibitors via pharmacophore and QSAR analysis followed by in silico screening

Taha, M. O., Bustanji, Y. K., Al‐Bakri, A. G., Yousef, A., Zalloum, W. A., Almasri, I. M., & Atallah, N. (2006) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2006.08.008 · Cited by 86 · see citing works

Combining Ligand-Based Pharmacophore Modeling, Quantitative Structure−Activity Relationship Analysis and in Silico Screening for the Discovery of New Potent Hormone Sensitive Lipase Inhibitors

Taha, M. O., Dahabiyeh, L. A., Bustanji, Y. K., Zalloum, H. M., & Saleh, S. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm800718k · Cited by 84 · see citing works

Analysis of Data Fusion Methods in Virtual Screening: Similarity and Group Fusion

Whittle, M., Gillet, V. J., Willett, P., & Loesel, J. (2006) · Journal of Chemical Information and Modeling · doi:10.1021/ci0496144 · Cited by 83 · see citing works

Enhancing the Effectiveness of Similarity-Based Virtual Screening Using Nearest-Neighbor Information

Hert, J., Willett, P., Wilton, D. J., Acklin, P., Azzaoui, K., Jacoby, E., & Schuffenhauer, A. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm050316n · Cited by 81 · see citing works

Comparison of Ligand- and Structure-Based Virtual Screening on the DUD Data Set

von Korff, M., Freyss, J., & Sander, T. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci800303k · Cited by 80 · see citing works

A Similarity‐based Data‐fusion Approach to the Visual Characterization and Comparison of Compound Databases

Medina‐Franco, J. L., Maggiora, G. M., Giulianotti, M. A., Pinilla, C., & Houghten, R. A. (2007) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2007.00579.x · Cited by 79 · see citing works

A Virtual Screening Approach to Finding Novel and Potent Antagonists at the Melanin-Concentrating Hormone 1 Receptor

Clark, D. E., Higgs, C. J., Wren, S. P., Dyke, H. J., Wong, M. H. L., Norman, D., Lockey, P. M., & Roach, A. G. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm040762v · Cited by 79 · see citing works

Chemical substructures in drug discovery

Merlot, C., Domine, D., Cleva, C., & Church, D. J. (2003) · Drug Discovery Today · doi:10.1016/s1359-6446(03)02740-5 · Cited by 78 · see citing works

Computational chemistry-driven decision making in lead generation

Schnecke, V., & Boström, J. (2006) · Drug Discovery Today · doi:10.1016/s1359-6446(05)03703-7 · Cited by 77 · see citing works

Multifingerprint Based Similarity Searches for Targeted Class Compound Selection

Kogej, T., Engkvist, O., Blomberg, N., & Mureşan, S. (2006) · Journal of Chemical Information and Modeling · doi:10.1021/ci0504723 · Cited by 76 · see citing works

Ligand-Based Virtual Screening Using Bayesian Networks

Abdo, A., Chen, B., Mueller, C., Salim, N. B., & Willett, P. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci100090p · Cited by 75 · see citing works

Scanning Structure–Activity Relationships with Structure–Activity Similarity and Related Maps: From Consensus Activity Cliffs to Selectivity Switches

Medina‐Franco, J. L. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300362x · Cited by 74 · see citing works

Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures

Tian, S., Sun, H., Li, Y., Pan, P., Li, D., & Hou, T. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400382r · Cited by 74 · see citing works

Enhancing the Effectiveness of Ligand‐Based Virtual Screening Using Data Fusion

Willett, P. (2006) · QSAR & Combinatorial Science · doi:10.1002/qsar.200610084 · Cited by 70 · see citing works

Discovery of new MurF inhibitors via pharmacophore modeling and QSAR analysis followed by in-silico screening

Taha, M. O., Atallah, N., Al‐Bakri, A. G., Paradis‐Bleau, C., Zalloum, H. M., Younis, K. S., & Lévesque, R. C. (2007) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2007.10.076 · Cited by 69 · see citing works

Integrating molecular design resources within modern drug discovery research: the Roche experience

Ståhl, M., Guba, W., & Kansy, M. (2006) · Drug Discovery Today · doi:10.1016/j.drudis.2006.02.008 · Cited by 69 · see citing works

Chemical Fragments as Foundations for Understanding Target Space and Activity Prediction

Sutherland, J. J., Higgs, R. E., Watson, I., & Vieth, M. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm701399f · Cited by 68 · see citing works

Analysis of a large food chemical database: chemical space, diversity, and complexity

Naveja, J. J., Rico‐Hidalgo, M. P., & Medina‐Franco, J. L. (2018) · F1000Research · doi:10.12688/f1000research.15440.2 · Cited by 68 · see citing works

A comparison of ligand based virtual screening methods and application to corticotropin releasing factor 1 receptor

Tresadern, G., Bemporad, D., & Howe, T. J. (2009) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2009.01.003 · Cited by 67 · see citing works

Comparison of Molecular Fingerprint Methods on the Basis of Biological Profile Data

Steffen, A., Kogej, T., Tyrchan, C., & Engkvist, O. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci800326z · Cited by 66 · see citing works

Ligand-Based Virtual Screening Using Graph Edit Distance as Molecular Similarity Measure

Garcia-Hernandez, C., Fernández, A., & Serratosa, F. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00820 · Cited by 65 · see citing works

Discovery of DPP IV Inhibitors by Pharmacophore Modeling and QSAR Analysis followed by in silico Screening

Almasri, I. M., Mohammad, M. K., & Taha, M. O. (2008) · ChemMedChem · doi:10.1002/cmdc.200800213 · Cited by 65 · see citing works

Pharmacophore Modeling, Quantitative Structure−Activity Relationship Analysis, and Shape-Complemented in Silico Screening Allow Access to Novel Influenza Neuraminidase Inhibitors

Abuhammad, A., & Taha, M. O. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci8003682 · Cited by 65 · see citing works

Big pharma screening collections: more of the same or unique libraries? The AstraZeneca–Bayer Pharma AG case

Kogej, T., Blomberg, N., Greasley, P. J., Mundt, S. M., Vainio, M. J., Schamberger, J., Schmidt, G. P., & Hüser, J. (2012) · Drug Discovery Today · doi:10.1016/j.drudis.2012.10.011 · Cited by 65 · see citing works

Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments

Good, A. C., Hermsmeier, M. A., & Hindle, S. A. (2004) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-004-4067-1 · Cited by 65 · see citing works

Elaborate ligand-based pharmacophore exploration and QSAR analysis guide the synthesis of novel pyridinium-based potent β-secretase inhibitory leads

Al-Nadaf, A. H., Sheikha, G. M. A., & Taha, M. O. (2010) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2010.03.043 · Cited by 64 · see citing works

Discovery of new cholesteryl ester transfer protein inhibitors via ligand-based pharmacophore modeling and QSAR analysis followed by synthetic exploration

Khalaf, R. A., Sheikha, G. M. A., Bustanji, Y. K., & Taha, M. O. (2010) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2009.12.070 · Cited by 64 · see citing works

Chemical Data Formats, Fingerprints, and Other Molecular Descriptions for Database Analysis and Searching

Bajusz, D., Rácz, A., & Héberger, K. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-409547-2.12345-5 · Cited by 63 · see citing works

Multi-Step In Silico Discovery of Natural Drugs against COVID-19 Targeting Main Protease

Elkaeed, E. B., Youssef, F. S., Eissa, I. H., Elkady, H., Alsfouk, A. A., Ashour, M. L., Hassab, M. A. E., Abou‐Seri, S. M., & Metwaly, A. M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23136912 · Cited by 59 · see citing works

A Comparison of Field-Based Similarity Searching Methods: CatShape, FBSS, and ROCS

Moffat, K., Gillet, V. J., Whittle, M., Bravi, G., & Leach, A. R. (2008) · Journal of Chemical Information and Modeling · doi:10.1021/ci700130j · Cited by 59 · see citing works

Hit-Directed Nearest-Neighbor Searching

Shanmugasundaram, V., Maggiora, G. M., & Lajiness, M. S. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm0493515 · Cited by 59 · see citing works

Thompson Sampling─An Efficient Method for Searching Ultralarge Synthesis on Demand Databases

Klarich, K., Goldman, B. B., Kramer, T. J., Riley, P., & Walters, W. P. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01790 · Cited by 57 · see citing works

Virtual screening strategies: Recent advances in the identification and design of anti-cancer agents

Kumar, V., Krishna, S., & Siddiqi, M. I. (2014) · Methods · doi:10.1016/j.ymeth.2014.08.010 · Cited by 56 · see citing works

Similarity searching

Stumpfe, D., & Bajorath, J. (2011) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.23 · Cited by 124 · see citing works

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 · see citing works

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 · see citing works

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 48 · see citing works

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 · see citing works