Let’s not forget tautomers.

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1

Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001) · Advanced Drug Delivery Reviews · doi:10.1016/s0169-409x(00)00129-0 · Cited by 18,139 · see citing works

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997) · Advanced Drug Delivery Reviews · doi:10.1016/s0169-409x(96)00423-1 · Cited by 11,484 · see citing works

Virtual high throughput screening (vHTS) - A perspective

Subramaniam, S., Mehrotra, M., & Gupta, D. (2008) · Bioinformation · doi:10.6026/97320630003014 · Cited by 3,509 · see citing works

Rules for ring closure

Baldwin, J. E. (1976) · Journal of the Chemical Society Chemical Communications · doi:10.1039/c39760000734 · Cited by 2,265 · see citing works

Calculation of Protein-Ligand Binding Affinities

Gilson, M. K., & Zhou, H. (2007) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.36.040306.132550 · Cited by 966 · see citing works

Modification of the NADH of the Isoniazid Target (InhA) from Mycobacterium tuberculosis

Rozwarski, D. A., Grant, G. A., Barton, D. H. R., Jacobs, W. R., & Sacchettini, J. C. (1998) · Science · doi:10.1126/science.279.5347.98 · Cited by 685 · see citing works

Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions

Wang, W., Donini, O., Reyes, C. M., & Kollman, P. A. (2001) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.30.1.211 · Cited by 549 · see citing works

Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 2. Prediction of blood–brain barrier penetration

Clark, D. E. (1999) · Journal of Pharmaceutical Sciences · doi:10.1021/js980402t · Cited by 523 · see citing works

Improved method for estimating water solubility from octanol/water partition coefficient

Meylan, W. M., Howard, P. H., & Boethling, R. S. (1996) · Environmental Toxicology and Chemistry · doi:10.1002/etc.5620150205 · Cited by 229 · see citing works

Solvent Effects and Chemical Reactivity

Tapia, O., & Bertrán, J. (2002) · Springer eBooks · doi:10.1007/0-306-46931-6 · Cited by 197 · see citing works

Structure Modification in Chemical Databases

Kenny, P. W., & Sadowski, J. (2005) · Methods and principles in medicinal chemistry · doi:10.1002/3527603743.ch11 · Cited by 182 · see citing works

Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping

Muchmore, S. W., Debe, D. A., Metz, J. T., Brown, S. P., Martin, Y. C., & Hajduk, P. J. (2008) · Journal of Chemical Information and Modeling · doi:10.1021/ci7004498 · Cited by 163 · see citing works

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.

Riccardi, D., Schaefer, P., & Cui, Q. (2005) · Journal of Physical Chemistry B · doi:10.1021/jp0517192 · Cited by 154 · see citing works

Comparison of the octanol/water partition coefficients calculated by ClogP®, ACDlogP and KowWin® to experimentally determined values

Machatha, S. G., & Yalkowsky, S. H. (2005) · International Journal of Pharmaceutics · doi:10.1016/j.ijpharm.2005.01.023 · Cited by 151 · see citing works

Tautomer Enumeration and Stability Prediction for Virtual Screening on Large Chemical Databases

Milletti, F., Storchi, L., Sforna, G., Cross, S., & Cruciani, G. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci800340j · Cited by 139 · see citing works

Predicting pKa

Lee, A. C., & Crippen, G. M. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci900209w · Cited by 131 · see citing works

The evolution of synthetic oral drug properties

Proudfoot, J. (2005) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2004.12.024 · Cited by 129 · see citing works

The 1.8-Å Crystal Structure of a Matrix Metalloproteinase 8-Barbiturate Inhibitor Complex Reveals a Previously Unobserved Mechanism for Collagenase Substrate Recognition

Brandstetter, H., Grams, F., Glitz, D., Lang, A., Huber, R., Bode, W., Krell, H., & Engh, R. A. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m007475200 · Cited by 127 · 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

Estimating log P with atom/fragments and water solubility with log P

Meylan, W. M., & Howard, P. H. (2000) · Perspectives in Drug Discovery and Design · doi:10.1023/a:1008715521862 · Cited by 120 · see citing works

Importance of Tautomers in the Chemical Behavior of Tetracyclines†

Duarte, H. A., Carvalho, S., Paniago, E. B., et al. (1999) · Journal of Pharmaceutical Sciences · doi:10.1021/js980181r · Cited by 120 · see citing works

First Principles Calculations of the Tautomers and p K a Values of 8-Oxoguanine: Implications for Mutagenicity and Repair

Jang, Y. H., Goddard, W. A., Noyes, K. T., Sowers, L. C., Hwang, S., & Chung, D. S. (2002) · Chemical Research in Toxicology · doi:10.1021/tx010146r · Cited by 112 · see citing works

Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of a Metal-Mediated Hydride Shift,

Fenn, T. D., Ringe, D., & Petsko, G. A. (2004) · Biochemistry · doi:10.1021/bi049812o · Cited by 108 · see citing works

Calculating log P(oct) with no missing fragments;The problem of estimating new interaction parameters

Leo, A. J., & Hoekman, D. A. (2000) · Perspectives in Drug Discovery and Design · doi:10.1023/a:1008739110753 · Cited by 105 · see citing works

Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects

Garcia‐Viloca, M., Alhambra, C., Truhlar, D. G., et al. (2002) · Journal of Computational Chemistry · doi:10.1002/jcc.10154 · Cited by 94 · see citing works

Solvent Effects and Chemical Reactivity

Subramanian, V. (2009) · CRC Press eBooks · doi:10.1201/9781420065442.ch26 · Cited by 93 · see citing works

First Principles Calculations of the p K a Values and Tautomers of Isoguanine and Xanthine

Rogstad, K. N., Jang, Y. H., Sowers, L. C., & Goddard, W. A. (2003) · Chemical Research in Toxicology · doi:10.1021/tx034068e · Cited by 88 · see citing works

The Impact of Tautomer Forms on Pharmacophore-Based Virtual Screening

Oellien, F., Cramer, J., Beyer, C., Ihlenfeldt, W., & Selzer, P. M. (2006) · Journal of Chemical Information and Modeling · doi:10.1021/ci060109b · Cited by 80 · see citing works

Crystal Structure of Macrophage Migration Inhibitory Factor Complexed with ( E )-2-Fluoro- p -hydroxycinnamate at 1.8 Å Resolution: Implications for Enzymatic Catalysis and Inhibition ,

Taylor, A. B., Johnson, W. H., Czerwiński, R., et al. (1999) · Biochemistry · doi:10.1021/bi9904048 · Cited by 73 · see citing works

Carbonic anhydrase inhibitors. Comparison of chlorthalidone, indapamide, trichloromethiazide, and furosemide X-ray crystal structures in adducts with isozyme II, when several water molecules make the difference

Temperini, C., Cecchi, A., Scozzafava, A., et al. (2008) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2008.12.023 · Cited by 66 · see citing works

Calculation of the geometry of a small protein using semiempirical methods

Stewart, J. J. P. (1997) · Journal of Molecular Structure THEOCHEM · doi:10.1016/s0166-1280(97)00050-x · Cited by 62 · see citing works

The Chemical Abstracts Service Chemical Registry System. I. General Design

Dittmar, P. G., Stobaugh, R. E., & Watson, C. E. (1976) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci60006a016 · Cited by 61 · see citing works

Differential Solvation and Tautomer Stability of a Model Base Pair within the Minor and Major Grooves of DNA

Dupradeau, F., Case, D. A., Yu, C., Jimenez, R., & Romesberg, F. E. (2005) · Journal of the American Chemical Society · doi:10.1021/ja054607x · Cited by 56 · see citing works

Estimation of Aqueous Solubility By The General Solubility Equation (GSE) The Easy Way

Sanghvi, T., Jain, N., Yang, G., et al. (2003) · QSAR & Combinatorial Science · doi:10.1002/qsar.200390020 · Cited by 52 · see citing works

Quantum chemical studies on tautomerism of barbituric acid in gas phase and in solution

Senthilkumar, K., & Kolandaivel, P. G. (2002) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1020273219651 · Cited by 48 · see citing works

A Simulation of the Catalytic Mechanism of Aspartylglucosaminidase Using ab Initio Quantum Mechanics and Molecular Dynamics

Peräkylä, M., & Kollman, P. A. (1997) · Journal of the American Chemical Society · doi:10.1021/ja9628967 · Cited by 47 · see citing works

Calculations of pK differences between structurally similar compounds

Rashin, A. A., Rabinowitz, J. R., & Banfelder, J. R. (1990) · Journal of the American Chemical Society · doi:10.1021/ja00167a006 · Cited by 46 · see citing works

(6,7-Dimethoxy-2,4-dihydroindeno[1,2-c]pyrazol-3-yl)phenylamines: Platelet-Derived Growth Factor Receptor Tyrosine Kinase Inhibitors with Broad Antiproliferative Activity against Tumor Cells

Ho, C. Y., Ludovici, D. W., Maharoof, U. S. M., et al. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm050680m · Cited by 35 · see citing works

Calculation of the tautomer ratio of histamine in aqueous solution using free energy perturbation methods: an in-depth study

Worth, G. A., & Richards, W. G. (1994) · Journal of the American Chemical Society · doi:10.1021/ja00080a028 · Cited by 33 · see citing works

Structure-based design and protein X-ray analysis of a protein kinase inhibitor

Furet, P., Meyer, T., Strauss, A., et al. (2002) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/s0960-894x(01)00715-6 · Cited by 33 · see citing works

Theoretical model-based equations for the linear free energy relations of the biological activity of ionizable substances. 1. Equilibrium-controlled potency

Martin, Y. C., & Hackbarth, J. J. (1976) · Journal of Medicinal Chemistry · doi:10.1021/jm00230a012 · Cited by 31 · see citing works

Co-crystallization of Two Tautomers: Crystal Structure of Isocytosine

McConnell, J. F., SHARMA, B. D., & Marsh, R. E. (1964) · Nature · doi:10.1038/203399a0 · Cited by 30 · see citing works

Enol−Enamine Tautomerism in Crystals of 1,3-Bis(pyridin-2-yl) Propan-2-one: A Combined Crystallographic and Quantum-Chemical Investigation of the Effect of Packing on Tautomerization Processes

Godsi, O., Turner, B., Suwinska, K., et al. (2004) · Journal of the American Chemical Society · doi:10.1021/ja046311h · Cited by 30 · see citing works

A phosphoinositide-binding sequence is shared by PH domain target molecules—a model for the binding of PH domains to proteins

Alberti, S. (1998) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19980401)31:1 · Cited by 29 · see citing works

Two tautomers in one crystal: 4(5)-nitro-5(4)-methoxyimidazole

Kubicki, M. (2004) · Acta Crystallographica Section B Structural Science · doi:10.1107/s0108768104003179 · Cited by 27 · see citing works

13C and 15N NMR study of 1,2,4-triazolo[1,5-a]pyrimidines with one tautomerism-introducing substituent

Kleinpeter, E., Thomas, S., & Fischer, G. (1995) · Journal of Molecular Structure · doi:10.1016/0022-2860(95)08918-l · Cited by 25 · see citing works

Tautomerism of heterocycles: Condensed five-six, five-five, and six-six ring systems with heteroatoms in both rings

Щербакова, І., Elguero, J., & KATRITZKY, A. R. (2000) · Advances in heterocyclic chemistry · doi:10.1016/s0065-2725(00)77004-8 · Cited by 25 · see citing works

Binding of the tautomeric forms of isoniazid-NAD adducts to the active site of the Mycobacterium tuberculosis enoyl-ACP reductase (InhA): A theoretical approach

Stigliani, J., Arnaud, P., Delaine, T., et al. (2008) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2008.09.006 · Cited by 24 · see citing works

Coexistence of both histidine tautomers in the solid state and stabilisation of the unfavourable Nδ–H form by intramolecular hydrogen bonding: crystalline l-His-Gly hemihydrate

Steiner, T., & Koellner, G. (1997) · Chemical Communications · doi:10.1039/a701807j · Cited by 23 · see citing works

Theoretical study of the keto-enol tautomerism in aqueous solutions

Karelson, M. M., Maran, U., & KATRITZKY, A. R. (1996) · Tetrahedron · doi:10.1016/0040-4020(96)00659-x · Cited by 20 · see citing works

Prediction of transition state structure in protein tyrosine phosphatase catalysis using a hybrid QM/MM potential

Hart, J. C., Burton, N. A., Hillier, I. H., et al. (1997) · Chemical Communications · doi:10.1039/a702304i · Cited by 20 · see citing works

The Influence of Variations of Ligand Protonation and Tautomerism on Protein−Ligand Recognition and Binding Energy Landscape

Todorov, N. P., Monthoux, P. H., & Alberts, I. L. (2006) · Journal of Chemical Information and Modeling · doi:10.1021/ci050071n · Cited by 20 · see citing works

Ring-chain tautomers of 6-substituted 2-acetylbenzoic acids

Finkelstein, J., Williams, T. C., Toome, V., et al. (1967) · The Journal of Organic Chemistry · doi:10.1021/jo01285a077 · Cited by 20 · see citing works

ACUTE TOXICITY OF THREE FIRE-RETARDANT AND TWO FIRE-SUPPRESSANT FOAM FORMULATIONS TO THE EARLY LIFE STAGES OF RAINBOW TROUT (ONCORHYNCHUS MYKISS)

Gaikowski, M. P., Hamilton, S. J., Buhl, K. J., McDonald, S. F., & Summers, C. H. (1996) · Environmental Toxicology and Chemistry · doi:10.1897/1551-5028(1996)015 · Cited by 20 · see citing works

Ring–Chain Tautomerism of Simplified Analogues of Isoniazid–NAD(P) Adducts: an Experimental and Theoretical Study

Delaine, T., Bernardes‐Génisson, V., Stigliani, J., et al. (2007) · European Journal of Organic Chemistry · doi:10.1002/ejoc.200600974 · Cited by 19 · see citing works

1,4-Dihydroindeno[1,2-c]pyrazoles as novel multitargeted receptor tyrosine kinase inhibitors

Dinges, J., Ashworth, K. L., Akritopolou-Zanze, I., et al. (2006) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2006.05.066 · Cited by 19 · see citing works

Insight into the specificity of thymidylate synthase from molecular dynamics and free energy perturbation calculations

Rastelli, G., Thomas, B. E., Kollman, P. A., et al. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00132a022 · Cited by 17 · see citing works

A theoretical study of pyrimidine photohydrates and a proposed mechanism for the mutagenic effect of ultraviolet light

Danilov, V. I., Stewart, J. J. P., Leś, A., et al. (2000) · Chemical Physics Letters · doi:10.1016/s0009-2614(00)00909-x · Cited by 13 · see citing works

Rare Tautomer Hypothesis Supported by Theoretical Studies: Ab Initio Investigations of Prototropic Tautomerism in the N-Methyl-P Base

Podolyan, Y., Gorb, L., & Leszczyński, J. (2005) · The Journal of Physical Chemistry A · doi:10.1021/jp0550412 · Cited by 12 · see citing works

Experimental and Computational Studies on Aminoguanidine Free Base, Monocation and Dication, Part I: The Crystal and Molecular Structure of Aminoguanidine Monohydrochloride and the ab Initio Structure of the Endiamine Tautomer of Aminoguanidine Free Base

Koskinen, J. T., Koskinen, M., Mutikainen, I., et al. (1996) · Zeitschrift für Naturforschung B · doi:10.1515/znb-1996-1215 · Cited by 12 · see citing works

Fast and accurate predictions of relative binding energies

Alex, A., & Finn, P. W. (1997) · Journal of Molecular Structure THEOCHEM · doi:10.1016/s0166-1280(97)00031-6 · Cited by 10 · see citing works

Simulation‐Based Predictions of Binding Affinities of Matrix Metalloproteinase Inhibitors

Khandelwal, A., Lukáčová, V., Kroll, D. M., Çömez, D., Raha, S., & Baláž, Š. (2004) · QSAR & Combinatorial Science · doi:10.1002/qsar.200430896 · Cited by 8 · see citing works

A comparative AM1 and ab initio study of the intramolecular proton transfer in tautomeric organic compounds

Maran, U., Karelson, M. M., & KATRITZKY, A. R. (1996) · International Journal of Quantum Chemistry · doi:10.1002/(sici)1097-461x(1996)60:8 · Cited by 6 · see citing works

Cocrystallization of two tautomers: 4-(1-{[4-(dimethylamino)benzylidene]hydrazono}ethyl)benzene-1,3-diol and 6-[(E)-1-{[4-(dimethylamino)benzylidene]hydrazino}ethylidene]-3-hydroxycyclohexa-2,4-dien-1-one (1/1)

Wu, Z., Ma, J., Wu, X.-W., et al. (2009) · Acta Crystallographica Section C Crystal Structure Communications · doi:10.1107/s0108270109006696 · Cited by 5 · see citing works

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

Chodera, J. D., & Mobley, D. L. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130318 · Cited by 531 · see citing works

Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges

Guedes, I. A., Pereira, F. S. S., & Dardenne, L. E. (2018) · Frontiers in Pharmacology · doi:10.3389/fphar.2018.01089 · Cited by 331 · see citing works

Intramolecular hydrogen bonding and intermolecular association of amino alcohols

Mulla, S. T., & Jose, C. I. (1986) · Journal of the Chemical Society Faraday Transactions 1 Physical Chemistry in Condensed Phases · doi:10.1039/f19868200691 · Cited by 14 · see citing works

Intramolecular Hydrogen Bond Interaction in Selected Diols

Plass, M., & Kolbe, A. (2003) · Zeitschrift für Physikalische Chemie · doi:10.1524/zpch.217.9.1085.20405 · Cited by 17 · see citing works

Infrared spectroscopic study of C7 intramolecular hydrogen bonds in peptides

Rao, C. P., Balaram, P., & Rao, C. N. R. (1983) · Biopolymers · doi:10.1002/bip.360220908 · Cited by 27 · see citing works

Intramolecular and intermolecular hydrogen bonds in aminophenols

Belkov, M. V., Ksendzov, G. A., Полозов, Г. И., et al. (2010) · Journal of Applied Spectroscopy · doi:10.1007/s10812-010-9359-8 · Cited by 9 · see citing works

Manifestation of intramolecular hydrogen bonds in the IR spectra of bioactive aminophenols

Ксендзова, Г. А., Полозов, Г. И., Skornyakov, I. V., Сорокин, В. Л., Tolstorozhev, G. B., Шадыро, О. И., & Yakunin, A. A. (2007) · Optics and Spectroscopy · doi:10.1134/s0030400x07040121 · Cited by 20 · see citing works