Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes

McGovern, Susan L.; Shoichet, Brian K.

doi:10.1021/jm0300330

Cited by 276Computational Drug Discovery MethodsProtein Structure and DynamicsReceptor Mechanisms and Signaling

Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes

McGovern, Susan L., Shoichet, Brian K.·2003·Journal of Medicinal Chemistry

DOI 10.1021/jm0300330

Open this paper in CoChat — free account

Abstract

Molecular docking uses the three-dimensional structure of a receptor to screen a small molecule database for potential ligands. The dependence of docking screens on the conformation of the binding site remains an open question. To evaluate the information loss that occurs as the active site conformation becomes less defined, a small molecule database was docked against the holo (ligand bound), apo, and homology modeled structures of 10 different enzyme binding sites. The holo and apo representations were crystallographic structures taken from the Protein Data Bank (PDB), and the homology-modeled structures were taken from the publicly available resource ModBase. The database docked was the MDL Drug Data Report (MDDR), a functionally annotated database of 95000 small molecules that contained at least 35 ligands for each of the 10 systems. In all sites, at least 99% of the molecules in the MDDR were treated as nonbinding decoys. For each system, the holo, apo, and modeled structures were used to screen the MDDR, and the ability of each structure to enrich the known ligands for that system over random selection was evaluated. The best overall enrichment was produced by the holo structure in seven systems, the apo structure in two systems, and the modeled structure in one system. These results suggest that the performance of the docking calculation is affected by the particular representation of the receptor used in the screen, and that the holo structure is the one most likely to yield the best discrimination between known ligands and decoy molecules, but important exceptions to this rule also emerge from this study. Although each of the holo, apo, and modeled conformations led to enrichment of known ligands in all systems, the enrichment did not always rise to a level judged to be sufficient to justify the effort of a docking screen. Using a 20-fold enrichment of known ligands over random selection as a rough guideline for what might be enough to justify a docking screen, the holo conformation of the enzyme met this criterion in eight of 10 sites, whereas the apo conformation met this criterion in only two sites and the modeled conformation in three.

Integrity signals

Registry

Crossref · 10.1021/jm0300330

Cites

65 of 65 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

The accuracy of binding geometries predicted by molecular docking to homology models strongly depends on the quality of the model, particularly in the binding site.
“The accuracy of the binding geometries predicted by molecular docking to homology models strongly depends on the quality of the model, particularly in the binding site22,40,41.”
From Modeling the binding of diverse ligands within the Ah receptor ligand binding domain (2019) · cites this paper as [41]

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works
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
A geometric approach to macromolecule-ligand interactions
Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., & Ferrin, T. E. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90153-x · Cited by 2,287 · see citing works
Automated docking with grid‐based energy evaluation
Meng, E. C., Shoichet, B. K., & Kuntz, I. D. (1992) · Journal of Computational Chemistry · doi:10.1002/jcc.540130412 · Cited by 956 · see citing works
Self-citation
Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.
Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, R. C., & Kraut, J. (1982) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)33497-5 · Cited by 746 · 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
Detailed Analysis of Scoring Functions for Virtual Screening
Ståhl, M., & Rarey, M. (2001) · Journal of Medicinal Chemistry · doi:10.1021/jm0003992 · Cited by 490 · see citing works
Calculation of electrostatic potentials in an enzyme active site
Gilson, M. K., & Honig, B. H. (1987) · Nature · doi:10.1038/330084a0 · Cited by 448 · see citing works
An Unlikely Sugar Substrate Site in the 1.65 Å Structure of the Human Aldose Reductase Holoenzyme Implicated in Diabetic Complications
Wilson, D. K., Bohren, K. M., Gabbay, K. H., & Quiocho, F. A. (1992) · Science · doi:10.1126/science.1621098 · Cited by 434 · see citing works
Molecular docking using shape descriptors
Shoichet, B. K., Kuntz, I. D., & Bodian, D. L. (1992) · Journal of Computational Chemistry · doi:10.1002/jcc.540130311 · Cited by 428 · see citing works
Self-citation
Statistical potentials for fold assessment
Melo, F., Sánchez, R., & Šali, A. (2002) · Protein Science · doi:10.1002/pro.110430 · Cited by 345 · see citing works
High-throughput docking for lead generation
Abagyan, R. A., & Totrov, M. M. (2001) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(00)00217-9 · Cited by 344 · see citing works
Discovery of Small-Molecule Inhibitors of Bcl-2 through Structure-Based Computer Screening
Enyedy, I. J., Ling, Y., Nacro, K., Tomita, Y. A., Wu, X., Cao, Y., Guo, R., Li, B., Zhu, X., Huang, Y. K., et al. (2001) · Journal of Medicinal Chemistry · doi:10.1021/jm010016f · Cited by 315 · see citing works
Molecular docking towards drug discovery
Gschwend, D. A., Good, A. C., & Kuntz, I. D. (1996) · Journal of Molecular Recognition · doi:10.1002/(sici)1099-1352(199603)9:2 · Cited by 302 · see citing works
Flexible ligand docking using conformational ensembles
Lorber, D. M., & Shoichet, B. K. (1998) · Protein Science · doi:10.1002/pro.5560070411 · Cited by 294 · see citing works
Self-citation
Resistance-Modifying Agents. 9. Synthesis and Biological Properties of Benzimidazole Inhibitors of the DNA Repair Enzyme Poly(ADP-ribose) Polymerase
White, A. W., Almassy, R. J., Calvert, A. H., et al. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm000950v · Cited by 288 · see citing works
Structure of the hirugen and hirulog 1 complexes of α-thrombin
Skrzypczak‐Jankun, E., Carperos, V. E., Ravichandran, K. G., Tulinsky, A., Westbrook, M. L., & Maraganore, J. M. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90939-4 · Cited by 261 · see citing works
Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate .cntdot. NADP+ ternary complex. substrate binding and a model for the transition state
Bystroff, C., Oatley, S. J., & Kraut, J. (1990) · Biochemistry · doi:10.1021/bi00465a018 · Cited by 243 · see citing works
A model binding site for testing scoring functions in molecular docking.
Wei, B. Q., Baase, W. A., Weaver, L. H., Matthews, B. W., & Shoichet, B. K. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00777-5 · Cited by 237 · see citing works
Self-citation
A ‘specificity’ pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil
Urzhumtsev, A., Favier, F., Mitschler, A., et al. (1997) · Structure · doi:10.1016/s0969-2126(97)00216-5 · Cited by 233 · see citing works
A new folate antimetabolite, 5,10-dideaza-5,6,7,8-tetrahydrofolate is a potent inhibitor of de novo purine synthesis
Beardsley, G. P., Moroson, B. A., Taylor, E. C., & Moran, R. G. (1989) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)31261-9 · Cited by 231 · see citing works
Strategic Pooling of Compounds for High-Throughput Screening
Hann, M. M., Hudson, B. D., Lewell, X. Q., Lifely, R., Miller, L., & Ramsden, N. G. (1999) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci990423o · Cited by 227 · see citing works
Prediction of electrostatic effects of engineering of protein charges
Sternberg, M. J. E., Hayes, F. R. F., Russell, A. J., et al. (1987) · Nature · doi:10.1038/330086a0 · Cited by 218 · see citing works
Matching chemistry and shape in molecular docking
Shoichet, B. K., & Kuntz, I. D. (1993) · Protein Engineering Design and Selection · doi:10.1093/protein/6.7.723 · Cited by 207 · see citing works
Self-citation
Structure-Based Generation of a New Class of Potent Cdk4 Inhibitors: New de Novo Design Strategy and Library Design
Honma, T., Hayashi, K., Aoyama, T., Hashimoto, N., Machida, T., Fukasawa, K., Iwama, T., Ikeura, C., Ikuta, M., Suzuki‐Takahashi, I., et al. (2001) · Journal of Medicinal Chemistry · doi:10.1021/jm0103256 · Cited by 203 · see citing works
Inhibitor and NAD+ Binding to Poly(ADP-ribose) Polymerase As Derived from Crystal Structures and Homology Modeling,
Ruf, A., de MURCIA, G., & Schulz, G. E. (1998) · Biochemistry · doi:10.1021/bi972383s · Cited by 199 · see citing works
Transition State Structure of Purine Nucleoside Phosphorylase and Principles of Atomic Motion in Enzymatic Catalysis,
Федоров, А. А., Shi, W., Kicska, G. A., et al. (2000) · Biochemistry · doi:10.1021/bi002499f · Cited by 190 · see citing works
MODBASE, a database of annotated comparative protein structure models
Pieper, U. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.255 · Cited by 175 · see citing works
Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D
Kick, E. K., Roe, D. C., Skillman, A. G., Liu, G., Ewing, T. J. A., Sun, Y., Kuntz, I. D., & Ellman, J. A. (1997) · Chemistry & Biology · doi:10.1016/s1074-5521(97)90073-9 · Cited by 154 · see citing works
Nucleic acid related compounds. 13
Robins, M. J., & Trip, E. M. (1974) · Tetrahedron Letters · doi:10.1016/s0040-4039(01)91909-4 · Cited by 140 · see citing works
Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength
Turner, M. A., Yuan, C., Borchardt, R. T., et al. (1998) · Nature Structural Biology · doi:10.1038/nsb0598-369 · Cited by 134 · see citing works
Structure-based design of inhibitors of purine nucleoside phosphorylase. 1. 9-(Arylmethyl) derivatives of 9-deazaguanine
Montgomery, J. A. J., Niwas, S., Rose, J. D., et al. (1993) · Journal of Medicinal Chemistry · doi:10.1021/jm00053a008 · Cited by 133 · see citing works
3D Structure of Torpedo californica Acetylcholinesterase Complexed with Huprine X at 2.1 Å Resolution: Kinetic and Molecular Dynamic Correlates,
Dvir, H., Wong, D. M., Harel, M., Barril, X., Orozco, M., Luque, F. J., Muñoz‐Torrero, D., Camps, P., Rosenberry, T. L., Silman, I., et al. (2002) · Biochemistry · doi:10.1021/bi011652i · Cited by 125 · see citing works
Dihydroisoquinolinones: the design and synthesis of a new series of potent inhibitors of poly(ADP-ribose) polymerase.
Suto, M. J., Turner, W. R., Arundel-Suto, C. M., Werbel, L. M., & Sebolt, J. S. (1991) · PubMed · Cited by 112 · see citing works
Crystal Structure ofS-Adenosylhomocysteine Hydrolase from Rat Liver,
Hu, Y., Komoto, J., Huang, Y., Gomi, T., Ogawa, H., Takata, Y., Fujioka, M., & Takusagawa, F. (1999) · Biochemistry · doi:10.1021/bi990332k · Cited by 109 · see citing works
Calf Spleen Purine Nucleoside Phosphorylase Complexed with Substrates and Substrate Analogues,
Mao, C., Cook, W. J., Zhou, M., Federov, A., Almo, S. C., & Ealick, S. E. (1998) · Biochemistry · doi:10.1021/bi9723919 · Cited by 104 · see citing works
Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase.
Almassy, R. J., Janson, C. A., Kan, C., et al. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.13.6114 · Cited by 96 · see citing works
The role of inhibitors of poly(ADP-ribose) polymerase as resistance-modifying agents in cancer therapy
Griffin, R., Curtin, N. J., Newell, D. R., et al. (1995) · Biochimie · doi:10.1016/0300-9084(96)88154-5 · Cited by 91 · see citing works
Design, Synthesis, and X-ray Crystal Structure of a Potent Dual Inhibitor of Thymidylate Synthase and Dihydrofolate Reductase as an Antitumor Agent
Gangjee, A., Yu, J., McGuire, J. J., et al. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm000200l · Cited by 91 · see citing works
Orientational sampling and rigid-body minimization in molecular docking revisited: On-the-fly optimization and degeneracy removal
Gschwend, D. A., & Kuntz, I. D. (1996) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf00402820 · Cited by 84 · see citing works
Two-Stage Method for Protein−Ligand Docking
Hoffmann, D. E., Kramer, B., Washio, T., Steinmetzer, T., Rarey, M., & Lengauer, T. (1999) · Journal of Medicinal Chemistry · doi:10.1021/jm991090p · Cited by 81 · see citing works
The additivity of substrate fragments in enzyme–ligand binding
Stout, T. J., Sage, C. R., & Stroud, R. M. (1998) · Structure · doi:10.1016/s0969-2126(98)00086-0 · Cited by 78 · see citing works
Novel inhibitors of Trypanosoma cruzi dihydrofolate reductase
Zuccotto, F., Zvelebil, M., Brun, R., et al. (2001) · European Journal of Medicinal Chemistry · doi:10.1016/s0223-5234(01)01235-1 · Cited by 70 · see citing works
Advances in the development of thrombin inhibitors
Steinmetzer, T., Hauptmann, J., & Stürzebecher, J. (2001) · Expert Opinion on Investigational Drugs · doi:10.1517/13543784.10.5.845 · Cited by 66 · see citing works
Protein–protein docking with multiple residue conformations and residue substitutions
Lorber, D. M., Udo, M. K., & Shoichet, B. K. (2002) · Protein Science · doi:10.1110/ps.2830102 · Cited by 63 · see citing works
Self-citation
A novel class of monoglutamated antifolates exhibits tight-binding inhibition of human glycinamide ribonucleotide formyltransferase and potent activity against solid tumors.
Habeck, L. L., Leitner, T. A., Shackelford, K. A., Gossett, L. S., Schultz, R. M., Andis, S. L., Shih, C., Grindey, G. B., & Mendelsohn, L. G. (1994) · PubMed · Cited by 58 · see citing works
Cloning of the gene encoding Leishmania donovaniS-adenosylhomocysteine hydrolase, a potential target for antiparasitic chemotherapy
Henderson, D. M., Hanson, S., Allen, T. E., et al. (1992) · Molecular and Biochemical Parasitology · doi:10.1016/0166-6851(92)90019-g · Cited by 57 · see citing works
Immunosuppression mediated by an inhibitor of S-adenosyl-L-homocysteine hydrolase. Prevention and treatment of collagen-induced arthritis.
Wolos, J. A., Frondorf, K. A., & Esser, R. E. (1993) · The Journal of Immunology · doi:10.4049/jimmunol.151.1.526 · Cited by 56 · see citing works
In silico discovery of novel Retinoic Acid Receptor agonist structures
Schapira, M., Raaka, B. M., Samuels, H. H., et al. (2001) · BMC Structural Biology · doi:10.1186/1472-6807-1-1 · Cited by 54 · see citing works
Structural basis for recognition of polyglutamyl folates by thymidylate synthase
Kamb, A., Finer-Moore, J. S., Calvert, A. H., et al. (1992) · Biochemistry · doi:10.1021/bi00156a005 · Cited by 54 · see citing works
Ligand-induced changes in the binding sites of proteins
Fradera, X., de la Cruz, X., da Silva, C. H. T. D. P., Gelpí, J. L., Luque, F. J., & Orozco, M. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.7.939 · Cited by 49 · see citing works
9-(Trans-2'-trans-3'-dihydroxycyclopent-4'-enyl) derivatives of adenine and 3-deazaadenine: potent inhibitors of bovine liver S-adenosylhomocysteine hydrolase
Narayanan, S. R., Keller, B. T., Borcherding, D. R., et al. (1988) · Journal of Medicinal Chemistry · doi:10.1021/jm00398a002 · Cited by 48 · see citing works
Nucleic Acid-Related Compounds. 84. Synthesis of 6'-(E and Z)-Halohomovinyl Derivatives of Adenosine, Inactivation of S-Adenosyl-L-homocysteine Hydrolase, and Correlation of Anticancer and Antiviral Potencies with Enzyme Inhibition
Wnuk, S. F., Yuan, C., Borchardt, R. T., et al. (1994) · Journal of Medicinal Chemistry · doi:10.1021/jm00047a015 · Cited by 47 · see citing works
Structure−Activity Relationships for a Class of Inhibitors of Purine Nucleoside Phosphorylase
Farutin, V., Masterson, L., Andricopulo, A. D., et al. (1999) · Journal of Medicinal Chemistry · doi:10.1021/jm990037y · Cited by 39 · see citing works
The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 å resolution: implications for a new mode of inhibition
Stout, T. J., & Stroud, R. M. (1996) · Structure · doi:10.1016/s0969-2126(96)00010-x · Cited by 38 · see citing works
New Insights into Inhibitor Design from the Crystal Structure and NMR Studies ofEscherichia coliGAR Transformylase in Complex with β-GAR and 10-Formyl-5,8,10-trideazafolic Acid,
Greasley, S. E., Yamashita, M. M., Cai, H. T., et al. (1999) · Biochemistry · doi:10.1021/bi991888a · Cited by 38 · see citing works
N10-Formyltetrahydrofolate is the formyl donor for glycinamide ribotide transformylase in Escherichia coli.
Dev, I. K., & Harvey, V. L. (1978) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)34710-5 · Cited by 37 · see citing works
7-Substituted 5-amino-1-cyclopropyl-6,8-difluoro-1,4-dihydro-4-oxo-3-quinolinecarboxylic acids: synthesis and biological activity of a new class of quinolone antibacterials
Domagala, J. M., Hagen, S. E., Heifetz, C. L., et al. (1988) · Journal of Medicinal Chemistry · doi:10.1021/jm00398a003 · Cited by 37 · see citing works
Structure-based design of inhibitors of purine nucleoside phosphorylase
Babu, Y. S., Ealick, S. E., Bugg, C. E., et al. (1995) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444994011704 · Cited by 34 · see citing works
Proton NMR sequential assignments and secondary structure analysis of human fibrinogen .gamma.-chain C-terminal residues 385-411
Mayo, K. H., Burke, C., Lindon, J. N., et al. (1990) · Biochemistry · doi:10.1021/bi00465a019 · Cited by 30 · see citing works
Phosphonate derivatives of N9-benzylguanine: a new class of potent purine nucleoside phosphorylase inhibitors
Halazy, S., Eggenspiller, A., Ehrhard, A., et al. (1992) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/s0960-894x(00)80157-2 · Cited by 27 · see citing works
Structure-Activity Relationships for a Collection of Structurally Diverse Inhibitors of Purine Nucleoside Phosphorylase.
Andricopulo, A. D., & Yunes, R. A. (2001) · Chemical and Pharmaceutical Bulletin · doi:10.1248/cpb.49.10 · Cited by 15 · see citing works
Folding the ribonuclease H domain of Moloney murine leukemia virus reverse transcriptase requires metal binding or a short N-terminal extension
Goedken, E. R., & Marqusee, S. (1998) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19981001)33:1 · Cited by 11 · see citing works
Synthesis and in vitro acetylcholinesterase inhibitory activity of some 1-substituted analogues of velnacrine
Kapples, K. J., Shutske, G. M., Bores, G. M., et al. (1993) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/s0960-894x(01)80765-4 · Cited by 3 · see citing works
Naphthalenylsulfonyl-hydantoins as aldose reductase inhibitors
Malamas, M., Sestanj, K., & Millen, J. (1991) · European Journal of Medicinal Chemistry · doi:10.1016/0223-5234(91)90096-6 · Cited by 3 · see citing works

Flagged first, then by citations

Sorted by citations

Benchmarking sets for molecular docking.
Huang, N., Shoichet, B. K., & Irwin, J. J. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm0608356 · Cited by 1,318 · see citing works
Self-citation
A practical guide to large-scale docking
Bender, B. J., Gahbauer, S., Luttens, A., Lyu, J., Webb, C. M., Stein, R. M., Fink, E. A., Balius, T. E., Carlsson, J., Irwin, J. J., et al. (2021) · Nature Protocols · doi:10.1038/s41596-021-00597-z · Cited by 546 · see citing works
Self-citation
Evaluation and optimization of virtual screening workflows with DEKOIS 2.0 – A public library of challenging docking benchmark sets.
Bauer, M. R., Ibrahim, T. M., Vogel, S. M., & Boeckler, F. M. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400115b · Cited by 200 · see citing works
Molecular Docking Screens Using Comparative Models of Proteins
Fan, H., Irwin, J. J., Webb, B. M., Klebe, G., Shoichet, B. K., & Sali, A. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci9003706 · Cited by 135 · see citing works
Self-citation
Modeling the binding of diverse ligands within the Ah receptor ligand binding domain
Giani Tagliabue, S., Faber, S. C., Motta, S., Denison, M. S., & Bonati, L. (2019) · Scientific Reports · doi:10.1038/s41598-019-47138-z · Cited by 106 · see citing works
Predicting the accuracy of protein–ligand docking on homology models
Bordogna, A., Pandini, A., & Bonati, L. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21601 · Cited by 107 · see citing works
Benchmarking data sets for the evaluation of virtual ligand screening methods: review and perspectives.
Lagarde, N., Zagury, J.-F., & Montes, M. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00090 · Cited by 85 · see citing works
New Aryl Hydrocarbon Receptor Homology Model Targeted To Improve Docking Reliability
Motto, I., Bordogna, A., Soshilov, A. A., Denison, M. S., & Bonati, L. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci2001617 · Cited by 80 · see citing works
Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms
Bonati, L., Corrada, D., Giani Tagliabue, S., & Motta, S. (2017) · Current Opinion in Toxicology · doi:10.1016/j.cotox.2017.01.011 · Cited by 27 · see citing works
Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug Design
Nagaraju, M., McGowan, L. C., & Hamelberg, D. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci300432w · Cited by 18 · see citing works
Leveraging AlphaFold2 structural space exploration for generating drug target structures in structure-based virtual screening
Uchikawa, K., Furui, K., & Ohue, M. (2025) · Biochemistry and Biophysics Reports · doi:10.1016/j.bbrep.2025.102110 · Cited by 1 · see citing works

Integrated Control and Docking Mechanism for Docking-Undocking Drones in the Air
Dohi, R., & Higashi, Y. (2022) · IEEE Region 10 Conference (TENCON) · doi:10.1109/tencon55691.2022.9978033 · Cited by 2 · see citing works
Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide
Alogheli, H., Olanders, G., Schaal, W., Brandt, P., & Karlén, A. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00443 · Cited by 83 · see citing works
GAsDock: a new approach for rapid flexible docking based on an improved multi-population genetic algorithm
Li, H., Li, C., Gui, C., Luo, X., Chen, K., Shen, J., Wang, X., & Jiang, H. (2004) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2004.06.091 · Cited by 56 · see citing works
Prediction of Protein-compound Complex Structures by Docking Simulation
Fukunishi, Y. (2011) · Seibutsu Butsuri · doi:10.2142/biophys.51.252
Protein docking prediction using predicted protein-protein interface
Li, B., & Kihara, D. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-7 · Cited by 75 · see citing works

Authors: McGovern, S. L., & Shoichet, B. K.
Affiliations: Northwestern University (US)
Corresponding author: Shoichet, Brian K.
ORCID: McGovern, Susan L.
Shoichet, Brian K.
Venue: Journal of Medicinal Chemistry
Publisher: American Chemical Society (ACS)
Published: 2003-06-05
Volume: 46
Issue: 14
Pages: 2895-2907
ISSN: 0022-2623 (ISSN-L)
1520-4804
DOI: 10.1021/jm0300330
OpenAlex: W2145722722
Cited by: 276
References: 65
Citations by year: 2026: 5 · 2025: 11 · 2024: 13 · 2023: 10 · 2022: 9 · 2021: 11 · 2020: 9 · 2019: 8 · 2018: 8 · 2017: 10 · 2016: 6 · 2015: 18 · 2014: 16 · 2013: 16 · 2012: 13
FWCI: 11.37
Type: journal article
Language: en
Open access: closed
Locations: Journal of Medicinal Chemistry (publishedVersion)
PubMed (publishedVersion)
Funders: National Institute of General Medical Sciences (T32 GM 08061, GM59957, R01GM059957, T32GM008061)
Topics: Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
Keywords: information decay, apo conformation, homology modeling, decoy discrimination
MeSH terms: Animals, Apoenzymes, Binding Sites, Enzymes, Humans, Ligands, Models, Molecular, Protein Binding, Protein Conformation, Crystallography, X-Ray, Holoenzymes, Quantitative Structure-Activity Relationship, Databases, Protein

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Cites

Cited by

Related

Record

About these checks