The Basis for Target‐Based Virtual Screening: Protein Structures

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

PROCHECK: a program to check the stereochemical quality of protein structures

Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993) · Journal of Applied Crystallography · doi:10.1107/s0021889892009944 · Cited by 24,581 · see citing works

The Cambridge Structural Database: a quarter of a million crystal structures and rising

Allen, F. H. (2002) · Acta Crystallographica Section B Structural Science · doi:10.1107/s0108768102003890 · Cited by 10,317 · see citing works

Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0897 · Cited by 6,763 · see citing works

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Davis, I., Leaver‐Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., Snoeyink, J. S., Richardson, J. S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm216 · Cited by 3,915 · see citing works

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

Goodford, P. J. (1985) · Journal of Medicinal Chemistry · doi:10.1021/jm00145a002 · Cited by 2,642 · see citing works

Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement

Engh, R., & Huber, R. (1991) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767391001071 · Cited by 2,497 · see citing works

Errors in protein structures

Hooft, R. W. W., Vriend, G., Sander, C., & Abola, E. E. (1996) · Nature · doi:10.1038/381272a0 · Cited by 2,180 · see citing works

Very fast empirical prediction and rationalization of protein pK a values

Li, H., Robertson, A. D., & Jensen, J. H. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20660 · Cited by 2,058 · see citing works

Improved Fourier coefficients for maps using phases from partial structures with errors

Read, R. J. (1986) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767386099622 · Cited by 1,885 · see citing works

Very fast prediction and rationalization of pKa values for protein–ligand complexes

Bas, D., Rogers, D. M., & Jensen, J. H. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22102 · Cited by 1,096 · see citing works

Rational design of inhibitors that bind to inactive kinase conformations

Liu, Y., & Gray, N. S. (2006) · Nature Chemical Biology · doi:10.1038/nchembio799 · Cited by 1,096 · see citing works

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

Bashford, D., & Karplus, M. (1990) · Biochemistry · doi:10.1021/bi00496a010 · Cited by 1,089 · see citing works

Retrieval of Crystallographically-Derived Molecular Geometry Information

Bruno, I. J., Cole, J. C., Kessler, M., Luo, J., MOTHERWELL, W. D. S., Purkis, L. H., Smith, B. R., Taylor, R., Cooper, R. I., Harris, S. E., et al. (2004) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci049780b · Cited by 987 · see citing works

Structure-based maximal affinity model predicts small-molecule druggability

Cheng, A. C., Coleman, R. G., Smyth, K. T., Cao, Q., Soulard, P., Caffrey, D. R., Salzberg, A. C., & Huang, E. S. (2007) · Nature Biotechnology · doi:10.1038/nbt1273 · Cited by 694 · see citing works

Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance

Hartshorn, M. J., Verdonk, M. L., Chessari, G., Brewerton, S. C., Mooij, W. T. M., Mortenson, P. N., & Murray, C. W. (2007) · Journal of Medicinal Chemistry · doi:10.1021/jm061277y · Cited by 623 · see citing works

PQS: a protein quaternary structure file server

Henrick, K. (1998) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(98)01253-5 · Cited by 540 · see citing works

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design

Ladbury, J. E. (1996) · Chemistry & Biology · doi:10.1016/s1074-5521(96)90164-7 · Cited by 521 · see citing works

Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: A platform for antiviral drug design

Goldgur, Y., Craigie, R., Cohen, G. H., Fujiwara, T., Yoshinaga, T., Fujishita, T., Sugimoto, H., Endo, T., Murai, H., & Davies, D. R. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.23.13040 · Cited by 496 · see citing works

Infrastructure for the life sciences: design and implementation of the UniProt website

Jain, E., Bairoch, A., Duvaud, S., Phan, I. Q., Redaschi, N., Süzek, B. E., Martin, M. J., McGarvey, P. B., & Gasteiger, E. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-136 · Cited by 485 · see citing works

Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding

Perola, E., & Charifson, P. S. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm030563w · Cited by 449 · see citing works

A new test set for validating predictions of protein–ligand interaction

Nissink, J. W. M., Murray, C. W., Hartshorn, M. J., Verdonk, M. L., Cole, J. C., & Taylor, R. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10232 · Cited by 425 · see citing works

Modeling water molecules in protein-ligand docking using GOLD.

Verdonk, M. L., Chessari, G., Cole, J. C., Hartshorn, M. J., Murray, C. W., Nissink, J. W. M., Taylor, R. D., & Taylor, R. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm050543p · Cited by 393 · see citing works

Application and Limitations of X‐ray Crystallographic Data in Structure‐Based Ligand and Drug Design

Davis, A. M., Teague, S. J., & Kleywegt, G. J. (2003) · Angewandte Chemie International Edition · doi:10.1002/anie.200200539 · Cited by 386 · see citing works

The Uppsala Electron-Density Server

Kleywegt, G. J., Harris, M. R., Zou, J.-Y., Taylor, T. C., Wählby, A., & Jones, T. A. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904013253 · Cited by 359 · see citing works

Crystal structure of the dimeric extracellular domain of human carbonic anhydrase XII, a bitopic membrane protein overexpressed in certain cancer tumor cells

Whittington, D. A., Waheed, A., Ulmasov, B., Shah, G. N., Grubb, J. H., Sly, W. S., & Christianson, D. W. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.161301298 · Cited by 350 · see citing works

[19] Free R value: Cross-validation in crystallography

Brünger, A. T. (1997) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(97)77021-6 · Cited by 328 · see citing works

Relibase: Design and Development of a Database for Comprehensive Analysis of Protein–Ligand Interactions

Hendlich, M., Bergner, A., Günther, J., & Klebe, G. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01408-0 · Cited by 324 · see citing works

Calculations of enzymic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes

Warshel, A. (1981) · Biochemistry · doi:10.1021/bi00514a028 · Cited by 319 · see citing works

Predicting druggable binding sites at the protein–protein interface

Fuller, J. C., Burgoyne, N. J., & Jackson, R. M. (2008) · Drug Discovery Today · doi:10.1016/j.drudis.2008.10.009 · Cited by 311 · see citing works

Predicting protein druggability

Hajduk, P. J., Huth, J. R., & Tse, C. (2005) · Drug Discovery Today · doi:10.1016/s1359-6446(05)03624-x · Cited by 289 · see citing works

Classification of Water Molecules in Protein Binding Sites

Barillari, C., Taylor, J., Viner, R., & Essex, J. W. (2007) · Journal of the American Chemical Society · doi:10.1021/ja066980q · Cited by 285 · see citing works

Variability in the pKa of histidine side‐chains correlates with burial within proteins

Edgcomb, S. P., & Murphy, K. P. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10177 · Cited by 206 · see citing works

Molecular Modeling Studies on Ligand Binding to Sialidase from Influenza Virus and the Mechanism of Catalysis

Taylor, N. R., & von Itzstein, M. (1994) · Journal of Medicinal Chemistry · doi:10.1021/jm00031a011 · Cited by 204 · see citing works

SuperStar: A Knowledge-based Approach for Identifying Interaction Sites in Proteins

Verdonk, M. L., Cole, J. C., & Taylor, R. S. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2809 · Cited by 198 · see citing works

The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU

Spinelli, S., LIU, Q., Alzari, P. M., Hirel, P. H., & Poljak, R. J. (1991) · Biochimie · doi:10.1016/0300-9084(91)90169-2 · Cited by 187 · see citing works

Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein−Ligand Docking Results

ten Brink, T., & Exner, T. E. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci800420z · Cited by 175 · see citing works

Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm

Raymer, M. L., Sanschagrin, P. C., Punch, W. F., Venkataraman, S., Goodman, E. D., & Kuhn, L. A. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0746 · Cited by 163 · see citing works

Limitations and lessons in the use of X-ray structural information in drug design

Davis, A. M., St-Gallay, S. A., & Kleywegt, G. J. (2008) · Drug Discovery Today · doi:10.1016/j.drudis.2008.06.006 · Cited by 162 · see citing works

WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes

García‐Sosa, A. T., Mancera, R. L., & Dean, P. M. (2003) · Journal of Molecular Modeling · doi:10.1007/s00894-003-0129-x · Cited by 130 · see citing works

Crystal Structures of the p21-Activated Kinases PAK4, PAK5, and PAK6 Reveal Catalytic Domain Plasticity of Active Group II PAKs

Eswaran, J., Lee, W. H., Debreczeni, J. E., Filippakopoulos, P., Turnbull, A., Fedorov, O., Deacon, S. W., Peterson, J. R., & Knapp, S. (2007) · Structure · doi:10.1016/j.str.2007.01.001 · Cited by 119 · see citing works

Protein Shape and Biological Control

Koshland, D. E. (1973) · Scientific American · doi:10.1038/scientificamerican1073-52 · Cited by 103 · see citing works

Superstar: improved knowledge-based interaction fields for protein binding sites11Edited by R. Huber

Verdonk, M. L., Cole, J. C., Watson, P., Gillet, V. J., & Willett, P. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4452 · Cited by 97 · see citing works

Aquaculture in Offshore Zones

Goudey, C. A. (2006) · Science · doi:10.1126/science.314.5807.1875c · Cited by 91 · see citing works

An empirical model for electrostatic interactions in proteins incorporating multiple geometry‐dependent dielectric constants

Wisz, M. S., & Hellinga, H. W. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10332 · Cited by 90 · see citing works

Similarity-driven flexible ligand docking

Fradera, X., Knegtel, R. M. A., & Mestres, J. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20000901)40:4 · Cited by 89 · see citing works

Automated ligand placement and refinement with a combined force field and shape potential

Wlodek, S. T., Skillman, A. G., & Nicholls, A. O. (2006) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444906016076 · Cited by 82 · see citing works

Protonation Changes upon Ligand Binding to Trypsin and Thrombin: Structural Interpretation Based on pKa Calculations and ITC Experiments

Czodrowski, P., Sotriffer, C., & Klebe, G. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.01.022 · Cited by 78 · see citing works

Protein–Ligand Docking Virtual Screening with GOLD

Cole, J. C., Nissink, J. W. M., & Taylor, R. (2005) · Drug discovery series · doi:10.1201/9781420028775.ch15 · Cited by 67 · see citing works

Energetics of the protein-DNA-water interaction

Spyrakis, F., Cozzini, P., Bertoli, C., Marabotti, A., Kellogg, G. E., & Mozzarelli, A. (2007) · BMC Structural Biology · doi:10.1186/1472-6807-7-4 · Cited by 63 · see citing works

Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects

Bergner, A., G�nther, J., Hendlich, M., Klebe, G., & Verdonk, M. L. (2001) · Biopolymers · doi:10.1002/1097-0282(2001/2002)61:2 · Cited by 60 · see citing works

Crystal structure of annexin V with its ligand K-201 as a calcium channel activity inhibitor

Kaneko, N., Ago, H., Matsuda, R., Inagaki, E., & Miyano, M. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1375 · Cited by 60 · see citing works

On vital aid: the why, what and how of validation

Kleywegt, G. J. (2009) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744490900081x · Cited by 44 · see citing works

Quantifying energetic contributions to ground state destabilization

Anderson, V. E. (2004) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2004.09.026 · Cited by 31 · see citing works

2-Pyridyl P1′-Substituted Symmetry-Based Human Immunodeficiency Virus Protease Inhibitors (A-792611 and A-790742) with Potential for Convenient Dosing and Reduced Side Effects

DeGoey, D. A., Grampovnik, D. J., Flentge, C. A., Flosi, W. J., Chen, H.-J., Yeung, C. M., Randolph, J. T., Klein, L. L., Dekhtyar, T., Colletti, L. M., et al. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm900044w · Cited by 29 · see citing works

Discovery of Thrombin Inhibitor Fragments from Chemical Microarray Screening

Neumann, T., Junker, H.-D., Keil, O., Burkert, K., Ottleben, H., Gamer, J., Sekul, R., Deppe, H., Feurer, A., Tomandl, D., et al. (2005) · Letters in Drug Design & Discovery · doi:10.2174/157018005774717343 · Cited by 24 · see citing works

Discovery of Thrombin Inhibitor Fragments from Chemical Microarray Screening

Neumann, T., Junker, H.-D., Keil, O., Burkert, K., Ottleben, H., Gamer, J., Sekul, R., Deppe, H., Feurer, A., Tomandl, D., et al. (2006) · Letters in Drug Design & Discovery · doi:10.2210/pdb2bvr/pdb · Cited by 21 · 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

Case-controlled structure validation

Read, R. J., & Kleywegt, G. J. (2009) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444908041085 · Cited by 19 · 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

Exploring different approaches to improve the success of drug discovery and development projects: a review

Kiriiri, G. K., Njogu, P., & Mwangi, A. (2020) · Future Journal of Pharmaceutical Sciences · doi:10.1186/s43094-020-00047-9 · Cited by 236 · see citing works

Fundamental considerations in drug design

Mahapatra, M. K., & Karuppasamy, M. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-90608-1.00005-8 · Cited by 36 · see citing works

Empirical Scoring Functions for Affinity Prediction of Protein‐ligand Complexes

Pason, L. P., & Sotriffer, C. (2016) · Molecular Informatics · doi:10.1002/minf.201600048 · Cited by 33 · see citing works

Protein Preparation Automatic Protocol for High-Throughput Inverse Virtual Screening: Accelerating the Target Identification by Computational Methods

Vita, S. D., Lauro, G., Ruggiero, D., Terracciano, S., Riccio, R., & Bifulco, G. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00428 · Cited by 26 · see citing works

Application of Virtual Screening Approaches for the Identification of Small Molecule Inhibitors of the Methyllysine Reader Protein Spindlin1

Luise, C., & Robaa, D. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8630-9_21 · Cited by 6 · see citing works

(How to) Profit from Molecular Dynamics-based Ensemble Docking

von Grafenstein, S., Fuchs, J. E., & Liedl, K. R. (2014) · Challenges and advances in computational chemistry and physics · doi:10.1007/978-94-017-9257-8_15 · Cited by 4 · see citing works

Pharmacophore searching: A potential solution for correcting unknown ligands (UNK) labelling errors in Protein Data Bank (PDB’S)

Ibrahim, M., Lapthorn, A. J., & Ibrahim, M. (2017) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2017.03.021 · Cited by 2 · see citing works

Optimisation de méthodes de criblage virtuel et synthèse de molécules à visée thérapeutique pour le traitement des maladies auto-immunes.

Nasr, N. B. (2014) · doi:10.70675/de51bc89z33fez456fz9467z959329cc603b

Structure-Based Virtual Screening

Schlosser, J., & Schlosser, J. (2016)

Recent Advances in Drug Discovery Research Using Structure‐Based Virtual Screening Techniques: Examples of Success for Diverse Protein Targets

Ghosh, S., Nie, A., An, J., & Huang, Z. (2006) · doi:10.1002/9780470131862.ch2

Target‐Based Virtual Screening on Small‐Molecule Protein Binding Sites

Heinke, R., Uciechowska, U., Jung, M., & Sippl, W. (2011) · Methods and principles in medicinal chemistry · doi:10.1002/9783527633326.ch15

Virtuální screening

Svozil, D. (2017) · ASEP

Virtual Screening

Svozil, D. (2017) · Chemické listy