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Protein–ligand docking: Current status and future challenges

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Molecular Recognition and Docking Algorithms

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A review of protein-small molecule docking methods

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

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Synthesis, characterization, in silico ADMET prediction, and protein binding analysis of a novel zinc(II) Schiff-base complex: Application of multi-spectroscopic and computational techniques

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Calixarene-based phosphinic acids as inhibitors of protein tyrosine phosphatases

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Four new guaiane sesquiterpenoids from agarwood of Aquilaria filaria

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Novel pyridinium based ionic liquids with amide tethers: Microwave assisted synthesis, molecular docking and anticancer studies

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Inhibition of Alzheimer’s amyloid-β42 peptide aggregation by a bi-functional bis-tryptoline triazole: key insights from molecular dynamics simulations

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Exploring the DNA binding efficacy of Cobalt(II) and Copper(II) complexes of hydroxamic acids and explicating their anti-cancer propensity

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Discovery of dihydroxyindole-2-carboxylic acid derivatives as dual allosteric HIV-1 Integrase and Reverse Transcriptase associated Ribonuclease H inhibitors

Esposito, F., Sechi, M., Pala, N., Sanna, A., Koneru, P. C., Kvaratskhelia, M., Naesens, L. M. J., Corona, A., Grandi, N., Santo, R. D., et al. (2019) · Antiviral Research · doi:10.1016/j.antiviral.2019.104671 · Cited by 24

A Review on Molecular Docking on HDAC Isoforms: Novel Tool for Designing Selective Inhibitors

Drakontaeidi, A., & Pontiki, E. A. (2023) · Pharmaceuticals · doi:10.3390/ph16121639 · Cited by 24

The Discodermolide Hairpin Structure Flows from Conformationally Stable Modular Motifs

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Nitromethylene Neonicotinoids Analogues with Tetrahydropyrimidine Fixed cis-Configuration: Synthesis, Insecticidal Activities, and Molecular Docking Studies

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Efficient and Robust Analysis of Biomacromolecular Flexibility Using Ensembles of Network Topologies Based on Fuzzy Noncovalent Constraints

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Comprehensive structural and functional characterization of Mycobacterium tuberculosis UDP-NAG enolpyruvyl transferase (Mtb-MurA) and prediction of its accurate binding affinities with inhibitors

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Polymorphic Signature of the Anti-inflammatory Activity of 2,2′-{[1,2-Phenylenebis(methylene)]bis(sulfanediyl)}bis(4,6-dimethylnicotinonitrile)

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Interaction of small molecules with human tyrosinase: A surface plasmon resonance and molecular docking study

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Classical Density Functional Theory for Molecular Systems

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Chiral separation and modeling of quinolones on teicoplanin macrocyclic glycopeptide antibiotics CSP

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Hydrophobicity-oriented drug design (HODD) of new human 4-hydroxyphenylpyruvate dioxygenase inhibitors

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EFFICIENT SYNTHESIS OF CHLORO CHALCONES UNDER ULTRASOUND IRRADIATION, THEIR ANTICANCER ACTIVITIES AND MOLECULAR DOCKING STUDIES

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Rational modification of Mannich base-type derivatives as novel antichagasic compounds: Synthesis, in vitro and in vivo evaluation

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Chiral resolution of four stereomers and simulation studies of newly synthesized antibacterial agents having two chiral centers

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Molecular Docking on FPGA and GPU Platforms

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Development of the Fluorescent BiosensorhCalmodulin (hCaM)L39C-monobromobimane(mBBr)/V91C-mBBr, a Novel Tool for Discovering New Calmodulin Inhibitors and Detecting Calcium

González‐Andrade, M., Rivera‐Chávez, J., Sosa‐Peinado, A., Figueroa, M., Rodríguez‐Sotres, R., & Mata, R. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm200167g · Cited by 23

Novel carbazolyl–thiazolyl–chromone and carbazolyl–thiazolyl–pyrazole hybrids: synthesis, cytotoxicity evaluation and molecular docking studies

Hassanin, N. M., Tarik El-Sayed, A. L. I., Assiri, M. A., & Abdel‐Kariem, S. M. (2024) · RSC Advances · doi:10.1039/d4ra03188a · Cited by 22

Molecular Dynamics Simulation Study and Hybrid Pharmacophore Model Development in Human LTA4H Inhibitor Design

Thangapandian, S., John, S., Arooj, M., & Lee, K. W. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034593 · Cited by 22

Engineering of CYP106A2 for steroid 9α- and 6β-hydroxylation

Nikolaus, J., Nguyen, K. T., Virus, C., Riehm, J. L., Hutter, M. C., & Bernhardt, R. (2017) · Steroids · doi:10.1016/j.steroids.2017.01.005 · Cited by 22

Evaluation of in silico ADMET analysis and human serum albumin interactions of a new lanthanum(III) complex by spectroscopic and molecular modeling studies

Shahraki, S., Shiri, F., & Saeidifar, M. (2017) · Inorganica Chimica Acta · doi:10.1016/j.ica.2017.04.023 · Cited by 22

Exploring isoxsuprine hydrochloride binding with human serum albumin in the presence of folic acid and ascorbic acid using multispectroscopic and molecular modeling methods

Shiri, F., Shahraki, S., Shahriyar, A., & Majd, M. H. (2017) · Journal of Photochemistry and Photobiology B Biology · doi:10.1016/j.jphotobiol.2017.04.007 · Cited by 22

Pharmacophore Mapping Approach for Drug Target Identification: A Chemical Synthesis and in Silico Study on Novel Thiadiazole Compounds

Meshram, R. J. (2017) · JOURNAL OF CLINICAL AND DIAGNOSTIC RESEARCH · doi:10.7860/jcdr/2017/22761.9925 · Cited by 22

Enhanced Antibacterial Activity of Ent-Labdane Derivatives of Salvic Acid (7α-Hydroxy-8(17)-ent-Labden-15-Oic Acid): Effect of Lipophilicity and the Hydrogen Bonding Role in Bacterial Membrane Interaction

Echeverría, J., Urzúa, A., Sanhueza, L., & Wilkens, M. (2017) · Molecules · doi:10.3390/molecules22071039 · Cited by 22

Strategies of Virtual Screening in Medicinal Chemistry

Passeri, G. I., Trisciuzzi, D., Alberga, D., Siragusa, L., Leonetti, F., Mangiatordi, G. F., & Nicolotti, O. (2017) · International Journal of Quantitative Structure-Property Relationships · doi:10.4018/ijqspr.2018010108 · Cited by 22

An α-helix mimetic oligopyridylamide, ADH-31, modulates Aβ 42 monomer aggregation and destabilizes protofibril structures: insights from molecular dynamics simulations

Kaur, A., Goyal, D., & Goyal, B. (2020) · Physical Chemistry Chemical Physics · doi:10.1039/d0cp04672h · Cited by 22

G-quadruplex binding properties of a potent PARP-1 inhibitor derived from 7-azaindole-1-carboxamide

Dallavalle, S., Musso, L., Artali, R., Aviñó, A. M., Scaglioni, L., Eritja, R., Gargallo, R., & Mazzini, S. (2021) · Scientific Reports · doi:10.1038/s41598-021-83474-9 · Cited by 21

Risperidone/Randomly Methylated β-Cyclodextrin Inclusion Complex—Compatibility Study with Pharmaceutical Excipients

Sbârcea, L., Tănase, I.-M., Ledeţi, A., Cîrcioban, D., Vlase, G., Barvinschi, P., Miclau, M., Văruț, R. M., Suciu, O., & Ledeţi, I. (2021) · Molecules · doi:10.3390/molecules26061690 · Cited by 22

Molecular docking and dynamic simulations of benzimidazoles with beta-tubulins

Rao, C. M. M. P. (2021) · Bioinformation · doi:10.6026//97320630017404 · Cited by 22

Exploring the therapeutic nature of limonoids and triterpenoids against SARS-CoV-2 by targeting nsp13, nsp14, and nsp15 through molecular docking and dynamics simulations

Vardhan, S., & Sahoo, S. K. (2021) · Journal of Traditional and Complementary Medicine · doi:10.1016/j.jtcme.2021.12.002 · Cited by 22

Design, Synthesis, and Fungicidal Evaluation of Novel N -Methoxy Pyrazole-4-Carboxamides as Potent Succinate Dehydrogenase Inhibitors

Li, H., Liu, Z., Dong, Y., Wang, Y., & Zhu, X. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.2c07031 · Cited by 22

Investigation of new 2-aryl substituted Benzothiopyrano[4,3-d]pyrimidines as kinase inhibitors targeting vascular endothelial growth factor receptor 2

Salerno, S., Marini, A. M., Fornaciari, G., Simorini, F., Motta, C. L., Taliani, S., Sartini, S., Settimo, F. D., García‐Argáez, A. N., Gia, O. M., et al. (2015) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2015.08.027 · Cited by 22

Prediction and validation of apoptosis through cytochrome P450 activation by benzo[a]pyrene

Das, D. N., Panda, P. K., Mukhopadhyay, S., Sinha, N., Mallick, B., Behera, B., Maiti, T. K., & Bhutia, S. K. (2013) · Chemico-Biological Interactions · doi:10.1016/j.cbi.2013.11.005 · Cited by 22

Insight into the binding interactions of CYP450 aromatase inhibitors with their target enzyme: a combined molecular docking and molecular dynamics study

Galeazzi, R., & Massaccesi, L. (2011) · Journal of Molecular Modeling · doi:10.1007/s00894-011-1144-y · Cited by 21

Predicting Inactive Conformations of Protein Kinases Using Active Structures: Conformational Selection of Type-II Inhibitors

Xu, M., Yu, L., Wan, B., Yu, L., & Huang, Q. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022644 · Cited by 22

Enrichment Factor Analyses on G-Protein Coupled Receptors with Known Crystal Structure

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Molecular modelling and multisimplex optimization of tocotrienol-rich Self Emulsified Drug Delivery Systems

Alayoubi, A. Y., Satyanarayanajois, S. D., Sylvester, P. W., & Nazzal, S. (2012) · International Journal of Pharmaceutics · doi:10.1016/j.ijpharm.2012.01.049 · Cited by 22

Synthesis and antibacterial activity of (1-aryl-1, 2, 3-triazol-4-yl) methyl esters of morpholine-3-carboxylic acid

Narsimha, S., Kumar, T. R., Nukala, S. K., Yakoob, S., & Reddy, N. V. (2014) · Medicinal Chemistry Research · doi:10.1007/s00044-014-1076-z · Cited by 22

Double Click Reaction for the Acquisition of a Highly Potent and Selective mPTPB Inhibitor

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Development of a novel class of B-RafV600E-selective inhibitors through virtual screening and hierarchical hit optimization

Kong, X., Qin, J., Li, Z., Vultur, A., Tong, L., Feng, E., Rajan, G. S., Liu, S., Lu, J., Liang, Z. T., et al. (2012) · Organic & Biomolecular Chemistry · doi:10.1039/c2ob26081f · Cited by 22

Synthesis and evaluation of coumarin/piperazine hybrids as acetylcholinesterase inhibitors

Zhang, J., & Jiang, C. (2018) · Medicinal Chemistry Research · doi:10.1007/s00044-018-2185-x · Cited by 22

Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations

Hu, X., Maffucci, I., & Contini, A. (2018) · Current Medicinal Chemistry · doi:10.2174/0929867325666180514110824 · Cited by 26

Development of New Photoswitchable Azobenzene Based γ-Aminobutyric Acid (GABA) Uptake Inhibitors with Distinctly Enhanced Potency upon Photoactivation

Lutz, T. A., Wein, T., Höfner, G. C., Pabel, J., Eder, M., Dine, J., & Wanner, K. T. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b00629 · Cited by 22

Hepatoprotective effect of bisbenzylisoquinoline alkaloid tiliamosine from Tiliacora racemosa in high-fat diet/diethylnitrosamine-induced non-alcoholic steatohepatitis

Darvin, S. S., Toppo, E., Esakkimuthu, S., Krishna, T. P. A., Ceasar, S. A., Stalin, A., Balakrishna, K., Muniappan, N., Pazhanivel, N., Mahaprabhu, R., et al. (2018) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2018.09.116 · Cited by 23

Synthesis and Evaluation of Halogenated 5-(2-Hydroxyphenyl)pyrazoles as Pseudilin Analogues Targeting the Enzyme IspD in the Methylerythritol Phosphate Pathway

Wang, J., Zhou, Y., Wang, X., Duan, L., Duan, J., Li, W., & Zhang, A. (2020) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.9b08057 · Cited by 22

One-Step Transformation from Rofecoxib to a COX-2 NIR Probe for Human Cancer Tissue/Organoid Targeted Bioimaging

Xie, L., Li, R., Zheng, B., Xie, Z., Fang, X., Dai, T., Wang, X., Li, L., Wang, L., Cuny, G. D., et al. (2021) · ACS Applied Bio Materials · doi:10.1021/acsabm.0c01634 · Cited by 22

Orientational switching of protein conformation as a function of nanoparticle curvature and their geometrical fitting

Khan, S., Gupta, A., Chaudhary, A., & Nandi, C. K. (2014) · The Journal of Chemical Physics · doi:10.1063/1.4893441 · Cited by 21

In silico description of differential enantioselectivity in methoxychlor O-demethylation by CYP2C enzymes

Bikádi, Z., & Hazai, E. (2008) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2008.06.001 · Cited by 22

New synthetic chitosan Schiff bases bearing pyranoquinolinone or benzonaphthyridine and their silver nanoparticles derivatives with potential activity as antioxidant and molecular docking study for EGFR inhibitors

Hassan, S. M., Morsy, J. M., Hassanin, H. M., Othman, E. S., & Mostafa, M. A. (2024) · RSC Advances · doi:10.1039/d4ra05117c · Cited by 21

Beyond Topoisomerase Inhibition: Antitumor 1,4‐Naphthoquinones as Potential Inhibitors of Human Monoamine Oxidase

Cerqueira, E. C., Netz, P. A., do Canto, V. P., Pinto, A. C., & Follmer, C. (2013) · Chemical Biology & Drug Design · doi:10.1111/cbdd.12255 · Cited by 21

Synthesis, Cytotoxicity Evaluation and Molecular Docking Studyof N-Phenylpyrazoline Derivatives

Suma, A. A. T., Wahyuningsih, T. D., & Mustofa, M. (2019) · Indonesian Journal of Chemistry · doi:10.22146/ijc.45777 · Cited by 21

Genome-Wide Analysis and Expression Profiling of Rice Hybrid Proline-Rich Proteins in Response to Biotic and Abiotic Stresses, and Hormone Treatment

Kapoor, R., Kumar, G., Arya, P., Jaswal, R., Jain, P., Singh, K., & Sharma, T. R. (2019) · Plants · doi:10.3390/plants8090343 · Cited by 21

The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions

Radaeva, M., Dong, X., & Cherkasov, A. R. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00325 · Cited by 22

Encapsulation of Risperidone by Methylated β-Cyclodextrins: Physicochemical and Molecular Modeling Studies

Sbârcea, L., Tănase, I.-M., Ledeţi, A., Cîrcioban, D., Vlase, G., Barvinschi, P., Miclau, M., Văruţ, R.-M., Trandafirescu, C. M., & Ledeţi, I. (2020) · Molecules · doi:10.3390/molecules25235694 · Cited by 21

Formulation and modification of physicochemical parameters of p-Coumaric acid by cyclodextrin nanosponges

Kumar, A., V, & Rao, R. (2022) · Journal of Inclusion Phenomena and Macrocyclic Chemistry · doi:10.1007/s10847-021-01121-2 · Cited by 21

Dual modulators of aggregation and dissociation of amyloid beta and tau: In vitro, in vivo, and in silico studies of Uncaria rhynchophylla and its bioactive components

Kim, S., Nam, Y., Shin, S. J., Prajapati, R., Shin, S. M., Kim, M., Kim, H. S., Leem, S. H., Kim, T., Park, Y., et al. (2022) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2022.113865 · Cited by 22

Equilibrium and DFT modeling studies for the biosorption of Safranin O dye from water samples using Bacillus subtilis biosorbent

Çetinkaya, S., Kaya, S., Aksu, A., Çetintaş, H. İ., Jalbani, N. S., Erkan, S., & Marzouki, R. (2022) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2022.134761 · Cited by 21

Novel trisubstituted acridines as human telomeric quadruplex binding ligands

Ungvarský, J., Plšíková, J., Janovec, L., Kovaĺ, J., Mikeš, J., Mikešová, L., Harvanová, D., Fedoročko, P., Kristián, P., Kašpárková, J., et al. (2014) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2014.07.010 · Cited by 22

Synthesis, structures and urease inhibition studies of dimeric copper(II) complexes of Schiff bases derived from glycine

Gou, Y., Yu, M., Li, Y., Peng, Y., & Wu, C. (2013) · Inorganica Chimica Acta · doi:10.1016/j.ica.2013.03.045 · Cited by 21

Role of the active site residues arginine-216 and arginine-237 in the substrate specificity of mammalian d-aspartate oxidase

Katane, M., Saitoh, Y., Maeda, K., Hanai, T., Sekine, M., Furuchi, T., & Homma, H. (2010) · Amino Acids · doi:10.1007/s00726-010-0658-4 · Cited by 21

Dictyostatin Flexibility Bridges Conformations in Solution and in the β-Tubulin Taxane Binding Site

Jogalekar, A. S., Damodaran, K., Kriel, F. H., Jung, W., Alcaraz, A. A., Zhong, S., Curran, D. P., & Snyder, J. P. (2011) · Journal of the American Chemical Society · doi:10.1021/ja1023817 · Cited by 21

New in silico insights into the inhibition of RNAP II by α-amanitin and the protective effect mediated by effective antidotes

Garcia, J., Carvalho, A. T. P., Dourado, D. F. A. R., Baptista, P. C., Bastos, M. D. L., & Carvalho, F. D. (2014) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2014.05.002 · Cited by 21

Tuning RNA Interference by Enhancing siRNA/PAZ Recognition

Gaglione, M., Potenza, N., Fabio, G. D., Romanucci, V., Mosca, N., Russo, A., Novellino, E., Cosconati, S., & Messere, A. (2012) · ACS Medicinal Chemistry Letters · doi:10.1021/ml300284b · Cited by 21

Protein–ligand docking using fitness learning-based artificial bee colony with proximity stimuli

Uehara, S., Fujimoto, K. J., & Tanaka, S. (2015) · Physical Chemistry Chemical Physics · doi:10.1039/c5cp01394a · Cited by 21

Tamoxifen, an anticancer drug, is an activator of human aldehyde dehydrogenase 1 A 1

Belmont-Díaz, J., Calleja, L. F., Yoval‐Sánchez, B., & Rodríguez‐Zavala, J. S. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24709 · Cited by 21

Synthesis, Insecticidal Activity, and Molecular Docking Studies of Nitenpyram Analogues with a Flexible Ester Arm Anchored on Tetrahydropyrimidine Ring

Sun, C., Xu, X., Xu, Y. X., Yan, D., Fang, T., & Liu, T. (2011) · Journal of Agricultural and Food Chemistry · doi:10.1021/jf1049563 · Cited by 21

Design and Synthesis of 2-Pyridone Based Flexible Dimers and Their Conformational Study through X-ray Diffraction and Density Functional Theory: Perspective of Cyclooxygenase-2 Inhibition

Rai, S. K., Khanam, S., Khanna, R. S., & Tewari, A. K. (2015) · Crystal Growth & Design · doi:10.1021/cg501793v · Cited by 21

In silico docking studies of non-azadirachtin limonoids against ecdysone receptor of Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae)

Yadav, R. P., Ibrahim, K. S., Gurusubramanian, G., & Kumar, N. S. (2015) · Medicinal Chemistry Research · doi:10.1007/s00044-015-1320-1 · Cited by 21

Two Binding Geometries for Risperidone in Dopamine D3 Receptors: Insights on the Fast-Off Mechanism through Docking, Quantum Biochemistry, and Molecular Dynamics Simulations

Zanatta, G., Nunes, G. D., BEZERRA, E. M., da COSTA, R. F., Martins, A. M. C., Caetano, E. W. S., Freire, V. N., & Gottfried, C. (2016) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.6b00074 · Cited by 22

Molecular insights into the inhibitory mechanism of rifamycin SV against β2–microglobulin aggregation: A molecular dynamics simulation study

Narang, S. S., Shuaib, S., & Goyal, B. (2017) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2017.04.086 · Cited by 21

Antiquorum Sensing Activity of Seed Oils from Oleaginous Plants and Protective Effect During Challenge with Chromobacterium violaceum

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Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease

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Rapid Optimization of the Metabolic Stability of a Human Immunodeficiency Virus Type-1 Capsid Inhibitor Using a Multistep Computational Workflow

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Polyamines: Naturally occurring small molecule modulators of electrostatic protein–protein interactions

Berwanger, A., Eyrisch, S., Schuster, I., Helms, V., & Bernhardt, R. (2009) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2009.10.007 · Cited by 22

Homology modeling of LmxMPK4 of Leishmania mexicana and virtual screening of potent inhibitors against it

Gupta, C. L., Khan, M. K. A., Khan, M. F., & Tiwari, A. K. (2013) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-013-0164-y · Cited by 21

Receptor Chemoprint Derived Pharmacophore Model for Development of CAIX Inhibitors

Islam, K. K. A. (2014) · Journal of Carcinogenesis & Mutagenesis · doi:10.4172/2157-2518.s8-003 · Cited by 21

Copper(II) complexes with N,O-donor azo-Schiff base ligands: Synthesis, structure, DFT studies, molecular docking, anticancer and antimicrobial activity

Kahraman, S., Hepokur, C., Erci, F., Erkan, S., Cetin, S., Köse, M., & Kurtoğlu, M. (2025) · Polyhedron · doi:10.1016/j.poly.2025.117393 · Cited by 20

Compound prioritization from inverse docking experiment using receptor‐centric and ligand‐centric methods: a case study onPlasmodium falciparumFab enzymes

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Metabolites from the entophytic fungus Sporormiella minimoides isolated from Hintonia latiflora

Leyte‐Lugo, M., Figueroa, M., González, M. D. C., Glenn, A. E., González‐Andrade, M., & Mata, R. (2013) · Phytochemistry · doi:10.1016/j.phytochem.2013.09.006 · Cited by 20

Discovery of bis-aromatic ring neonicotinoid analogues fixed as cis-configuration: Synthesis, insecticidal activities, and molecular docking studies

Sun, C., Jin, J., Jun, Z., Wang, H., Yang, D., & Xing, J. (2010) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2010.04.050 · Cited by 20

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges

Nishikawa, N., Han, K., Wu, X.-W., Tofoleanu, F., & Brooks, B. (2018) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-018-0166-2 · Cited by 18

1,4,7-Triazacyclononane Restores the Activity of β-Lactam Antibiotics against Metallo-β-Lactamase-Producing Enterobacteriaceae : Exploration of Potential Metallo-β-Lactamase Inhibitors

Somboro, A. M., Amoako, D. G., Sekyere, J. O., Kumalo, H. M., Khan, R. B., Bester, L. A., & Essack, S. Y. (2018) · Applied and Environmental Microbiology · doi:10.1128/aem.02077-18 · Cited by 20

Protein acetylation effects on enzyme activity and metabolic pathway fluxes

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Insulin Complexation with Cyclodextrins—A Molecular Modeling Approach

Bucur, P., FÜLÖP, I. Z., & Sipos, E. (2022) · Molecules · doi:10.3390/molecules27020465 · Cited by 20

Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy

Tao, H., Zhao, X., Zhang, K., Lin, P., & Huang, S. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac486 · Cited by 19

Exploring molecular structure (monomer & dimer), spectroscopic (FT-IR, FT-Raman, UV-Vis, NMR), TG/DTA, antibacterial and molecular docking investigation on 2-[2,3-dichloro-4-(2-methylidenebutanoyl)phenoxy] acetic acid by DFT and wavefunction analysis

Asokan, S., Sebastian, S. S. H. R., Karthikeyan, B., Xavier, S., Raman, R. G., Silvan, S., Margreat, S. S., & Sagayaraj, R. (2024) · Chemical Physics Impact · doi:10.1016/j.chphi.2024.100497 · Cited by 20

Phosphonate monoesters on a thiacalix[4]arene framework as potential inhibitors of protein tyrosine phosphatase 1B

Trush, V. V., Kharchenko, S. G., Tanchuk, V. Y., Kаlchеnkо, V. I., & Vovk, A. I. (2015) · Organic & Biomolecular Chemistry · doi:10.1039/c5ob01247c · Cited by 20

Structural basis of the anti-inflammatory activity of quercetin: inhibition of the 5-Hydroxytryptamine Type 2 Receptor

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Effects of Acrylamide on the Activity and Structure of Human Brain Creatine Kinase

Sheng, Q., Zou, H.-C., Lü, Z.-R., Zou, F., Park, Y., Yan, Y., & Yao, S. (2009) · International Journal of Molecular Sciences · doi:10.3390/ijms10104210 · Cited by 20

Insight into ligand selectivity in HCV NS5B polymerase: molecular dynamics simulations, free energy decomposition and docking

Li, T., Froeyen, M., & Herdewijn, P. A. (2009) · Journal of Molecular Modeling · doi:10.1007/s00894-009-0519-9 · Cited by 20

In silico screening of chalcone derivatives as potential inhibitors of dihydrofolate reductase: Assessment using molecular docking, paired potential and molecular hydrophobic potential studies

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Flexibility and inhibitor binding in cdc25 phosphatases

Arantes, G. M. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22826 · Cited by 22

Epoxide‐Hydrolase‐Initiated Hydrolysis/Rearrangement Cascade of a Methylene‐Interrupted Bis‐Epoxide Yields Chiral THF Moieties without Involvement of a “Cyclase”

Ueberbacher, B. T., Oberdorfer, G., Gruber, K. F., & Faber, K. (2009) · ChemBioChem · doi:10.1002/cbic.200900176 · Cited by 20

Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment

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Synthesis and molecular docking studies of a new series of bipyrazol-yl-thiazol-ylidene-hydrazinecarbothioamide derivatives as potential antitubercular agents

Mogle, P. P., Meshram, R. J., Hese, S. V., Kamble, R. D., Kamble, S. S., Gacche, R. N., & Dawane, B. S. (2016) · MedChemComm · doi:10.1039/c6md00085a · Cited by 20

Software News and Update A Semiempirical Free Energy Force Field with Charge-Based Desolvation

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Software News and Update A Semiempirical Free Energy Force Field

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Molecular docking, estimating free energies of binding, and AutoDock's semi-empirical force field

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Simplified AutoDock force field for hydrated binding sites

Wojciechowski, M. (2017) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2017.09.016 · Cited by 17

A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking

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