Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., et al. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm0306430 · Cited by 10,057

Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes

Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm051256o · Cited by 7,012

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

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Docking and scoring in virtual screening for drug discovery: methods and applications

Kitchen, D. B., Decornez, H. Y., Furr, J. R., & Bajorath, J. (2004) · Nature Reviews Drug Discovery · doi:10.1038/nrd1549 · Cited by 4,354

HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187

Improved protein–ligand docking using GOLD

Verdonk, M. L., Cole, J. C., Hartshorn, M. J., Murray, C. W., & Taylor, R. D. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10465 · Cited by 3,139

PatchDock and SymmDock: servers for rigid and symmetric docking

Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki481 · Cited by 3,018

A Fast Flexible Docking Method using an Incremental Construction Algorithm

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MolDock: A New Technique for High-Accuracy Molecular Docking

Thomsen, R., & Christensen, M. H. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm051197e · Cited by 2,381

Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects

Sherman, W., Day, T., Jacobson, M. P., Friesner, R. A., & Farid, R. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm050540c · Cited by 2,089

Molecular docking analysis: Basic technique to predict drug-receptor interactions

Silakari, O., & Singh, P. K. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-820546-4.00006-4 · Cited by 30

Proteome-scale docking: myth and reality

Rognan, D. (2013) · Drug Discovery Today Technologies · doi:10.1016/j.ddtec.2013.01.003 · Cited by 25

Ligand-Receptor Affinities Computed by an Adapted Linear Interaction Model for Continuum Electrostatics and by Protein Conformational Averaging

Nunes-Alves, A., & Arantes, G. M. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci500301s · Cited by 18

Docking Methods for Virtual Screening: Principles and Recent Advances

Rognan, D. (2011) · Methods and principles in medicinal chemistry · doi:10.1002/9783527633326.ch6 · Cited by 27

Revolutionizing drug discovery: an AI-powered transformation of molecular docking

Fadahunsi, A. A., Uzoeto, H. O., Okoro, N. O., Cosmas, S., Durojaye, O. A., & Odiba, A. S. (2024) · Medicinal Chemistry Research · doi:10.1007/s00044-024-03253-9 · Cited by 28

Proteochemometric Modeling of the Bioactivity Spectra of HIV-1 Protease Inhibitors by Introducing Protein-Ligand Interaction Fingerprint

Huang, Q., Jin, H., Liu, Q., Wu, Q., Kang, H., Cao, Z., & Zhu, R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041698 · Cited by 23

CrystalDock: A Novel Approach to Fragment-Based Drug Design

Durrant, J. D., Friedman, A. J., & McCammon, J. A. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200357y · Cited by 24

Molecular Dynamic Simulations and Molecular Docking as a Potential Way for Designed New Inhibitor Drug without Resistance.

Aghajani, J., Farnia, P., Farnia, P., Ghanavi, J., & Velayati, A. A. (2022) · PubMed Central · Cited by 24

CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity

Wu, J., Chen, H., Cheng, M., & Xiong, H. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05503-w · Cited by 23

Post-docking virtual screening of diverse binding pockets: Comparative study using DOCK, AMMOS, X-Score and FRED scoring functions

Pencheva, T., Soumana, O. S., Pajeva, I. K., & Miteva, M. A. (2010) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2009.12.025 · Cited by 24

Molecular docking study investigating the possible mode of binding of C.I. Acid Red 73 with DNA

Guo, Y., Yue, Q., & Gao, B. (2011) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2011.03.009 · Cited by 23

Protein-ligand docking

Bottegoni, G. (2011) · Frontiers in bioscience · doi:10.2741/3854 · Cited by 27

Drug Discovery in Africa

Chibale, K., Masimirembwa, C. M., & Davies-Coleman, M. (2012) · Springer eBooks · doi:10.1007/978-3-642-28175-4 · Cited by 25

Role of Water in Ligand Binding to Maltose-Binding Protein: Insight from a New Docking Protocol Based on the 3D-RISM-KH Molecular Theory of Solvation

Huang, W., Blinov, N., Wishart, D. S., & Kovalenko, A. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci500520q · Cited by 24

C(X)CR in silico: Computer-aided prediction of chemokine receptor–ligand interactions

Roumen, L., Scholten, D. J., de Kruijf, P., de Esch, I. J. P., Leurs, R., & de Graaf, C. (2012) · Drug Discovery Today Technologies · doi:10.1016/j.ddtec.2012.05.002 · Cited by 23

Molecular modeling and in vitro study on pyrocatechol as potential pharmacophore of CD151 inhibitor

Akella, M., & Malla, R. R. (2020) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2020.107681 · Cited by 22

Machine Learning Scoring Functions Based on Random Forest and Support Vector Regression

Ballester, P. J. (2012) · Lecture notes in computer science · doi:10.1007/978-3-642-34123-6_2 · Cited by 22

Automated site preparation in physics‐based rescoring of receptor ligand complexes

Rapp, C. S., Schonbrun, C., Jacobson, M. P., Kalyanaraman, C., & Huang, N. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22415 · Cited by 22

Alpha-Glucosidase Folding During Urea Denaturation: Enzyme Kinetics and Computational Prediction

Wu, X.-Q., Wang, J., Lü, Z.-R., Tang, H., Park, D., Oh, S. H., Bhak, J., Shi, L., Park, Y., & Zou, F. (2009) · Applied Biochemistry and Biotechnology · doi:10.1007/s12010-009-8636-6 · Cited by 21

Some Trends in Chem(o)informatics

Warr, W. A. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-839-3_1 · Cited by 21

Covalent Simulations of Covalent/Irreversible Enzyme Inhibition in Drug Discovery: A Reliable Technical Protocol

Khan, S., Bjij, I., Olotu, F. A., Agoni, C., Adeniji, E. A., & Soliman, M. E. S. (2018) · Future Medicinal Chemistry · doi:10.4155/fmc-2017-0304 · Cited by 20

Mammalian Olfactory Receptors

Persuy, M., Sanz, G., Tromelin, A., Thomas‐Danguin, T., Gibrat, J.-F., & Pajot-Augy, E. (2014) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2014.11.001 · Cited by 22

Ligand entry pathways in the ligand binding domain of PPARγ receptor

Aci‐Sèche, S., Genest, M., & Garnier, N. (2011) · FEBS Letters · doi:10.1016/j.febslet.2011.07.014 · Cited by 20

Identification of novel prolyl oligopeptidase inhibitors from resin of Boswellia papyrifera (Del.) Hochst. and their mechanism: Virtual and biochemical studies

Khan, A., Waqas, M. S., Khan, M., Halim, S. A., Rehman, N. U., & Al‐Harrasi, A. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.06.001 · Cited by 20

Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction

Sulea, T. I., Hogues, H., & Purisima, E. O. (2011) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-011-9529-7 · Cited by 20

MoDock: A multi-objective strategy improves the accuracy for molecular docking

Gu, J., Yang, X., Kang, L., Wu, J., & Wang, X. (2015) · Algorithms for Molecular Biology · doi:10.1186/s13015-015-0034-8 · Cited by 21

New mimetic peptides inhibitors of Αβ aggregation. Molecular guidance for rational drug design

Barrera, E., Andújar, S. A., Hubin, E., Broersen, K., Kraan, I. M., Méndez, L., Delpiccolo, C. M. L., Masman, M. F., Rodríguez, A. M., & Enriz, R. D. (2015) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2015.03.042 · Cited by 20

Screening for the selective inhibitors of MMP-9 from natural products based on pharmacophore modeling and molecular docking in combination with bioassay experiment, hybrid QM/MM calculation, and MD simulation

Hou, J., Zou, Q. S., Wang, Y., Gao, Q., Yao, W., Yao, Q., & Zhang, J. (2018) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2018.1509019 · Cited by 20

Recognizing drug targets using evolutionary information: implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv

Ramakrishnan, G., Chandra, N. R., & Srinivasan, N. (2015) · Molecular BioSystems · doi:10.1039/c5mb00476d · Cited by 19

Target specific proteochemometric model development for BACE1 – protein flexibility and structural water are critical in virtual screening

Manoharan, P., Chennoju, K., & Ghoshal, N. (2015) · Molecular BioSystems · doi:10.1039/c5mb00088b · Cited by 19

Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015

Slynko, I., Silva, F. D., Bret, G., & Rognan, D. (2016) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-016-9930-3 · Cited by 20

Interactions of ketoamide inhibitors on HCV NS3/4A protease target: molecular docking studies

Wadood, A., Riaz, M., Jamal, S. B., & Shah, M. (2013) · Molecular Biology Reports · doi:10.1007/s11033-013-2867-x · Cited by 19

In Silico Veritas: The Pitfalls and Challenges of Predicting GPCR-Ligand Interactions

Roumen, L., Sanders, M. P. A., Vroling, B., de Esch, I. J. P., de Vlieg, J., Leurs, R., Klomp, J. P. G., Nabuurs, S. B., & de Graaf, C. (2011) · Pharmaceuticals · doi:10.3390/ph4091196 · Cited by 18

Robust optimization of scoring functions for a target class

Seifert, M. H. J. (2009) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-009-9276-1 · Cited by 18

Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge

Purisima, E. O., Corbeil, C. R., & Sulea, T. I. (2010) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-010-9341-9 · Cited by 18

Protein Ligand Docking in Drug Discovery

Brás, N. F., Cerqueira, N. M. F. S. A., Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2014) · Springer eBooks · doi:10.1007/978-3-319-09976-7_11 · Cited by 20

Torsional Energy Barriers of Biaryls Could Be Predicted by Electron Richness/Deficiency of Aromatic Rings; Advancement of Molecular Mechanics toward Atom-Type Independence

Wei, W., Champion, C., Liu, Z., Barigye, S. J., Labute, P., & Moitessier, N. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00585 · Cited by 17

Docking, Binding Free Energy Calculations and In Vitro Characterization of Pyrazine Linked 2-Aminobenzamides as Novel Class I Histone Deacetylase (HDAC) Inhibitors

Bülbül, E. F., Melesina, J., Ibrahim, H. S., Abdelsalam, M. A. M., Vecchio, A., Robaa, D., Zessin, M., Schutkowski, M., & Sippl, W. (2022) · Molecules · doi:10.3390/molecules27082526 · Cited by 19

Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation

Wright, J. S., Anderson, J. M., Shadnia, H., Durst, T., & Katzenellenbogen, J. A. (2013) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-013-9670-6 · Cited by 17

Modeling Reality for Optimal Docking of Small Molecules to Biological Targets

Corbeil, C. R., Therrien, É., & Moitessier, N. (2009) · Current Computer - Aided Drug Design · doi:10.2174/157340909789577856 · Cited by 17

Physics-Based Scoring of Protein–Ligand Interactions: Explicit Polarizability, Quantum Mechanics and Free Energies

Bryce, R. A. (2011) · Future Medicinal Chemistry · doi:10.4155/fmc.11.30 · Cited by 17

Scoring Functions for Protein–Ligand Interactions

Sotriffer, C. (2012) · Protein‐Ligand Interactions · doi:10.1002/9783527645947.ch12 · Cited by 16

Customizable Generation of Synthetically Accessible, Local Chemical Subspaces

Pottel, J., & Moitessier, N. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00648 · Cited by 16

Compounds in Indonesian Ginger Rhizome Extracts and Their Potential for Anti-Skin Aging Based on Molecular Docking

Asoka, S. F., Batubara, I., Lestari, A. R., Wahyuni, W. T., & Wahyudi, S. T. (2022) · Cosmetics · doi:10.3390/cosmetics9060128 · Cited by 16

NMR and Docking Calculations Reveal Novel Atomistic Selectivity of a Synthetic High-Affinity Free Fatty Acid vs. Free Fatty Acids in Sudlow’s Drug Binding Sites in Human Serum Albumin

Venianakis, T., Primikyri, A., Opatz, T., Petry, S., Papamokos, G., & Gerothanassis, I. P. (2023) · Molecules · doi:10.3390/molecules28247991 · Cited by 16

Cancer and Biotechnology: A Matchup that Should Never Slowdown

Hrout, A. A., Baig, B., Hilal‐Alnaqbi, A., & Amin, A. (2017) · Springer eBooks · doi:10.1007/978-3-319-53880-8_3 · Cited by 16

The Challenge of Affinity Prediction: Scoring Functions for Structure‐Based Virtual Screening

Sotriffer, C., & Matter, H. (2011) · Methods and principles in medicinal chemistry · doi:10.1002/9783527633326.ch7 · Cited by 16

A Review on Artificial Intelligence Approaches and Rational Approaches in Drug Discovery

Srivathsa, A. V., Sadashivappa, N. M., Hegde, A. K., Radha, S., Mahesh, A. R., Ammunje, D. N., Sen, D., Theivendren, P., Saravanan, G., Kunjiappan, S., et al. (2023) · Current Pharmaceutical Design · doi:10.2174/1381612829666230428110542 · Cited by 16

In Silico Docking: Protocols for Computational Exploration of Molecular Interactions

Mathur, N., Chandragiri, S. S., Sarita, S., Shandily, S., Santoki, K. M., Vadhavana, N. N., Shah, S., & Chandra, M. (2024) · Biomedical engineering · doi:10.5772/intechopen.1005527 · Cited by 17

EDGA: A Population Evolution Direction-Guided Genetic Algorithm for Protein–Ligand Docking

Guan, B., Zhang, C., & Ning, J. (2016) · Journal of Computational Biology · doi:10.1089/cmb.2015.0190 · Cited by 15

Application of Computational Techniques to Unravel Structure-Function Relationship and their Role in Therapeutic Development

Yadav, T. C., Srivastava, A., Dey, A., Kumar, N., Raghuwanshi, N., & Pruthi, V. (2018) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026619666181120142141 · Cited by 14

CRDOCK: An Ultrafast Multipurpose Protein–Ligand Docking Tool

Cortés-Cabrera, Á., Klett, J., Santos, H. G. D., Perona, A., Gil‐Redondo, R., Francis, S. M., Priego, E., Gago, F., & Morreale, A. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300194a · Cited by 15

Toward a Robust Search Method for the Protein-Drug Docking Problem

Sadjad, B. S., & Zsoldos, Z. (2010) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2010.70 · Cited by 15

In silico database screening of potential targets and pathways of compounds contained in plants used for psoriasis vulgaris

May, B. H., Deng, S., Zhang, A. L., Lu, C., & Xue, C. C. (2015) · Archives of Dermatological Research · doi:10.1007/s00403-015-1577-8 · Cited by 15

Docking and scoring: applications to drug discovery in the interactomics era

Grosdidier, S., & Fernández‐Recio, J. (2009) · Expert Opinion on Drug Discovery · doi:10.1517/17460440903002067 · Cited by 15

Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics

Iakovou, G., Hayward, S., & Laycock, S. D. (2015) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2015.06.003 · Cited by 14

A real-time proximity querying algorithm for haptic-based molecular docking

Iakovou, G., Hayward, S., & Laycock, S. D. (2014) · Faraday Discussions · doi:10.1039/c3fd00123g · Cited by 14

QM/MM Docking Strategy and Prime/MM-GBSA Calculation of Celecoxib Analogues as N-myristoyltransferase Inhibitors

Meena, N. C. K. (2015) · Virology & Mycology · doi:10.4172/2161-0517.1000141 · Cited by 14

An Efficient ABC_DE_Based Hybrid Algorithm for Protein–Ligand Docking

Guan, B., Zhang, C., & Zhao, Y. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19041181 · Cited by 14

Prospects for Discovering the Secondary Metabolites of Cordyceps Sensu Lato by the Integrated Strategy

Bibi, S., Wang, Y., Tang, D., Kamal, M. A., & Yu, H. (2019) · Medicinal Chemistry · doi:10.2174/1573406416666191227120425 · Cited by 14

Computational Perspectives into Plasmepsins Structure—Function Relationship: Implications to Inhibitors Design

Gil-Ley, A., Valiente, P. A., Pascutti, P. G., & Pons, T. (2011) · Journal of Tropical Medicine · doi:10.1155/2011/657483 · Cited by 14

Pharmacophore Identification and Pseudo-Receptor Modeling

Wolber, G., & Sippl, W. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-417205-0.00021-3 · Cited by 14

CIFDock : A novel CHARMM ‐based flexible receptor–flexible ligand docking protocol

Vankayala, S. L., Warrensford, L. C., Pittman, A. R., Pollard, B. C., Kearns, F. L., Larkin, J. D., & Woodcock, H. L. (2021) · Journal of Computational Chemistry · doi:10.1002/jcc.26759 · Cited by 13

Optimization of molecular docking scores with support vector rank regression

Wang, W., He, W., Zhou, X. F., & Chen, X. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24282 · Cited by 13

Elucidating Hyperconjugation from Electronegativity to Predict Drug Conformational Energy in a High Throughput Manner

Liu, Z., Pottel, J., Shahamat, M., Tomberg, A., Labute, P., & Moitessier, N. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00012 · Cited by 13

A Novel Fireworks Algorithm for the Protein-Ligand Docking on the AutoDock

Liu, Z., Jiang, D., Zhang, C., Zhao, H., Zhao, Q., & Zhang, B. (2019) · Mobile Networks and Applications · doi:10.1007/s11036-019-01412-6 · Cited by 13

Relating the shape of protein binding sites to binding affinity profiles: is there an association?

Simon, Z., Vigh-Smeller, M., Peragovics, Á., Csukly, G., Zahoránszky-Köhalmi, G., Rauscher, A. Á., Jelinek, B., Hári, P., Bitter, I., Málnási‐Csizmadia, A., et al. (2010) · BMC Structural Biology · doi:10.1186/1472-6807-10-32 · Cited by 13

Assessment of molecular binding of Hoechst 33258 analogues into DNA using docking and MM/GBSA approach

Issar, U., Kumari, T., & Kakkar, R. (2015) · Journal of Computational Science · doi:10.1016/j.jocs.2015.05.003 · Cited by 13

HopDock: a probabilistic search algorithm for decoy sampling in protein-protein docking

Hashmi, I., & Shehu, A. (2013) · Proteome Science · doi:10.1186/1477-5956-11-s1-s6 · Cited by 13

Importance of Computer-aided Drug Design in Modern Pharmaceutical Research

Agarwal, U., Tonk, R. K., & Paliwal, S. (2025) · Current Drug Discovery Technologies · doi:10.2174/0115701638361318241230073123 · Cited by 14

GUIDING PROTEIN DOCKING WITH GEOMETRIC AND EVOLUTIONARY INFORMATION

Hashmi, I., Akbal-Delibas, B., Haspel, N., & Shehu, A. (2012) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720012420085 · Cited by 12

RANK-ORDERING THE BINDING AFFINITY FOR FKBP12 AND H1N1 NEURAMINIDASE INHIBITORS IN THE COMBINATION OF A PROTEIN MODEL WITH DENSITY FUNCTIONAL THEORY

He, G., SHI, J., Chen, Y., CHEN, Y., Zhang, Q., Wang, M., & Liu, J. (2011) · Journal of Theoretical and Computational Chemistry · doi:10.1142/s0219633611006633 · Cited by 12

Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics

Iakovou, G., Hayward, S., & Laycock, S. D. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00051 · Cited by 12

Chem-bioinformatic approach for drug discovery

Ojha, H., Sethi, M., Kakkar, R., Sharma, M., Saini, M., & Pathak, M. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-821748-1.00005-1 · Cited by 13

Virtual Screening - models, methods and software systems

Lazarova, M. K. (2008) · Cited by 12

Theory of docking scores and its application to a customizable scoring function

Takahashi, O., Masuda, Y., Muroya, A., & Furuya, T. (2010) · SAR and QSAR in environmental research · doi:10.1080/1062936x.2010.502299 · Cited by 12

Evaluation of inhibitory effects of benzothiazole and 3-amino-benzothiazolium derivatives on DNA topoisomerase II by molecular modeling studies

Aki, E., Ertan‐Bolelli, T., Taşkın‐Tok, T., Öztürk, Ö., Ataei, S., Özen, Ç., Yıldız, İ., & Yalçın, İ. (2014) · SAR and QSAR in environmental research · doi:10.1080/1062936x.2014.923039 · Cited by 12

The Comparison of Docking Search Algorithms and Scoring Functions

Novič, M., Tibaut, T., Anderluh, M., Borišek, J., & Tomašič, T. (2016) · Advances in medical technologies and clinical practice book series · doi:10.4018/978-1-5225-0115-2.ch004 · Cited by 13

IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads

Al-Saadi, A., Alfè, D., Babuji, Y., Bhati, A. P., Blaiszik, B. J., Brace, A., Brettin, T. S., Chard, K., Chard, R., Clyde, A., et al. (2021) · Proceedings of the International Conference on Parallel Processing · doi:10.1145/3472456.3473524 · Cited by 33

Novel computational pipelines in antiviral structure‑based drug design (Review)

Diakou, I., Papakonstantinou, E., Papageorgiou, L., Pierouli, K., Dragoumani, K., Spandidos, D. A., Bacopoulou, F., Chrousos, G. P., Eliopoulos, E., & Vlachakis, D. (2022) · Biomedical Reports · doi:10.3892/br.2022.1580 · Cited by 13

Deep Generation Model Guided by the Docking Score for Active Molecular Design

Yang, Y., Hsieh, C., Kang, Y., Hou, T., Liu, H., & Yao, X. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00572 · Cited by 13

Using Machine Learning Methods to Predict Experimental High Throughput Screening Data

Mballo, C., & Makarenkov, V. (2010) · Combinatorial Chemistry & High Throughput Screening · doi:10.2174/138620710791292958 · Cited by 11

Performance of Protein–Ligand Docking with Simulated Chemical Shift Perturbations

ten Brink, T., Aguirre, C., Exner, T. E., & Krimm, I. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci500446s · Cited by 11

Antiviral Efficacy of Selected Natural Phytochemicals against SARS-CoV-2 Spike Glycoprotein Using Structure-Based Drug Designing

Aloufi, B. H., Snoussi, M., & Sulieman, A. M. E. (2022) · Molecules · doi:10.3390/molecules27082401 · Cited by 11

Discovery of Novel α4β2 Neuronal Nicotinic Receptor Modulators through Structure-Based Virtual Screening

Mahasenan, K. V., Pavlovicz, R. E., Henderson, B. J., González-Cestari, T. F., Yi, B., McKay, D. B., & Li, C. (2011) · ACS Medicinal Chemistry Letters · doi:10.1021/ml2001714 · Cited by 12

Studi In Silico Senyawa Alkaloid Herba Bakung Putih (Crinum Asiaticum L.) pada Penghambatan Enzim Siklooksigenase (COX)

Rachmania, R. A., Hariyanti, H., Zikriah, R., & Sultan, A. (2018) · Jurnal Kimia VALENSI · doi:10.15408/jkv.v4i2.7686 · Cited by 11

IMPROVING HOMOLOGY MODELS FOR PROTEIN-LIGAND BINDING SITES

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Docking and Scoring in Drug Discovery

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Docking Method for Drug Discovery

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