AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Particle swarm optimization

Kennedy, J., & Eberhart, R. (2002) · Proceedings of ICNN'95 - International Conference on Neural Networks · doi:10.1109/icnn.1995.488968 · Cited by 58,192

Adaptation in Natural and Artificial Systems

Holland, J. H. (1992) · The MIT Press eBooks · doi:10.7551/mitpress/1090.001.0001 · Cited by 47,340

Optimization by Simulated Annealing

Kirkpatrick, S., Gelatt, C. D., & Vecchi, M. P. (1983) · Science · doi:10.1126/science.220.4598.671 · Cited by 45,134

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21256 · Cited by 26,294

A new optimizer using particle swarm theory

Eberhart, R., & Kennedy, J. (2002) · MHS'95. Proceedings of the Sixth International Symposium on Micro Machine and Human Science · doi:10.1109/mhs.1995.494215 · Cited by 16,067

Numerical optimization

Braun, W. J., & Murdoch, D. J. (2021) · Cambridge University Press eBooks · doi:10.1017/9781108993456.011 · Cited by 14,099

Numerical Optimization

Nocedal, J., & Wright, S. J. (1999) · Springer eBooks · doi:10.1007/b98874 · Cited by 9,563

ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

Abagyan, R. A., Totrov, M. M., & Kuznetsov, D. (1994) · Journal of Computational Chemistry · doi:10.1002/jcc.540150503 · Cited by 1,718

The statistical-thermodynamic basis for computation of binding affinities: a critical review

Gilson, M. K., Given, J. A., Bush, B. L., & McCammon, J. A. (1997) · Biophysical Journal · doi:10.1016/s0006-3495(97)78756-3 · Cited by 1,222

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

Wang, R., Lai, L., & Wang, S. (2002) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1016357811882 · Cited by 1,185

Engineering and application of a biosensor with focused ligand specificity

Corte, D. D., van Beek, H. L., Syberg, F., Schallmey, M., Tobola, F., Cormann, K. U., Schlicker, C., Baumann, P. T., Krumbach, K., Sokolowsky, S., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18400-0 · Cited by 104

Flavonoid glycosides and their putative human metabolites as potential inhibitors of the SARS-CoV-2 main protease (Mpro) and RNA-dependent RNA polymerase (RdRp)

da Silva, F. M. A., da Silva, K. P. A., Oliveira, L. P., Costa, E. V., Koolen, H. H. F., Pinheiro, M. L. B., de Souza, A. Q. L., & de Souza, A. D. L. (2020) · Memórias do Instituto Oswaldo Cruz · doi:10.1590/0074-02760200207 · Cited by 104

Clean Grinding Technique: A Facile Synthesis and In Silico Antiviral Activity of Hydrazones, Pyrazoles, and Pyrazines Bearing Thiazole Moiety against SARS-CoV-2 Main Protease (Mpro)

Abu‐Melha, S., Edrees, M. M., Riyadh, S. M., Abdelaziz, M. R., Elfiky, A. A., & Gomha, S. M. (2020) · Molecules · doi:10.3390/molecules25194565 · Cited by 104

Integrated metabolomics and network pharmacology to reveal the mechanisms of hydroxysafflor yellow A against acute traumatic brain injury

Li, T., Zhang, W., Hu, E., Sun, Z., Li, P., Yu, Z., Zhu, X., Zheng, F., Xing, Z., Xia, Z., et al. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.01.033 · Cited by 102

Efficacy of Phytochemicals Derived from Avicennia officinalis for the Management of COVID-19: A Combined In Silico and Biochemical Study

Mahmud, S., Paul, G. K., Afroze, M., Islam, S., Gupta, S. B. R., Razu, M. H., Biswas, S., Zaman, S., Uddin, M. S., Khan, M., et al. (2021) · Molecules · doi:10.3390/molecules26082210 · Cited by 107

SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking

Murail, S., de Vries, S. J., Rey, J., Moroy, G., & Tufféry, P. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.716466 · Cited by 104

GC/MS Profiling, Anti-Collagenase, Anti-Elastase, Anti-Tyrosinase and Anti-Hyaluronidase Activities of a Stenocarpus sinuatus Leaves Extract

Younis, M. M., Ayoub, I. M., Mostafa, N. M., Hassab, M. A. E., Eldehna, W. M., Al‐Rashood, S. T., & Eldahshan, O. A. (2022) · Plants · doi:10.3390/plants11070918 · Cited by 104

Cryo-EM structure of human ATR-ATRIP complex

Rao, Q., Liu, M., Tian, Y., Wu, Z., Hao, Y., Song, L., Qin, Z., Ding, C., Wang, H., Wang, J., et al. (2017) · Cell Research · doi:10.1038/cr.2017.158 · Cited by 106

Combining molecular docking and molecular dynamics simulation to discover four novel umami peptides from tuna skeletal myosin with sensory evaluation validation

Zhao, S., Ma, S., Zhang, Y., Gao, M., Luo, Z., & Cai, S. (2023) · Food Chemistry · doi:10.1016/j.foodchem.2023.137331 · Cited by 104

Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design

Allen, W. J., & Rizzo, R. C. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci400534h · Cited by 107

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

Carlson, H. A., Smith, R. D., Damm‐Ganamet, K. L., Stuckey, J. A., Ahmed, A., Convery, M. A., Somers, D. O., Kranz, M., Elkins, P. A., Cui, G., et al. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00523 · Cited by 105

Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense

Liu, G., Ma, H., Xie, H., Ning, X., Guo, X. N., Fan, Z., Rajashekar, B., Arnaud, P., Offmann, B., & Picimbon, J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0154706 · Cited by 103

Activity of Novel Synthetic Peptides against Candida albicans

Lum, K. Y., Tay, S. T., Le, C. F., Lee, V. S., Sabri, N. H., Velayuthan, R. D., Hassan, H. H., & Sekaran, S. D. (2015) · Scientific Reports · doi:10.1038/srep09657 · Cited by 102

Using bacterial genomes and essential genes for the development of new antibiotics

Fields, F. R., Lee, S. W., & McConnell, M. J. (2016) · Biochemical Pharmacology · doi:10.1016/j.bcp.2016.12.002 · Cited by 103

Multi-spectroscopic and molecular modelling approach to investigate the interaction of riboflavin with human serum albumin

Alam, M. M., Qais, F. A., Ahmad, I., Alam, P., Khan, R. H., & Naseem, I. (2017) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2017.1298470 · Cited by 103

Multiple approaches to assess the effects of F-53B, a Chinese PFOS alternative, on thyroid endocrine disruption at environmentally relevant concentrations

Deng, M., Wu, Y., Xu, C., Jin, Y., He, X., Wan, J., Yu, X., Rao, H., & Tu, W. (2017) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2017.12.101 · Cited by 105

POAP: A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening

Ansar, S., & Vetrivel, U. (2018) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2018.02.012 · Cited by 101

Pyruvate dehydrogenase complex and lactate dehydrogenase are targets for therapy of acute liver failure

Ferriero, R., Nusco, E., Cegli, R. D., Carissimo, A., Manco, G., & Brunetti‐Pierri, N. (2018) · Journal of Hepatology · doi:10.1016/j.jhep.2018.03.016 · Cited by 103

Docking with SwissDock

Bitencourt‐Ferreira, G., & de Azevedo, W. F. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9752-7_12 · Cited by 103

Potential Drugs Targeting Early Innate Immune Evasion of SARS-Coronavirus 2 via 2’-O-Methylation of Viral RNA

Encinar, J. A., & Menéndez, J. A. (2020) · Viruses · doi:10.3390/v12050525 · Cited by 102

EDock: blind protein–ligand docking by replica-exchange monte carlo simulation

Zhang, W., Bell, E. W., Yin, M., & Zhang, Y. (2020) · Journal of Cheminformatics · doi:10.1186/s13321-020-00440-9 · Cited by 103

In silico molecular docking analysis for repurposing therapeutics against multiple proteins from SARS-CoV-2

Deshpande, R. R., Tiwari, A. P., Nyayanit, N., & Modak, M. A. (2020) · European Journal of Pharmacology · doi:10.1016/j.ejphar.2020.173430 · Cited by 108

5-((1H-imidazol-1-yl)methyl)quinolin-8-ol as potential antiviral SARS-CoV-2 candidate: Synthesis, crystal structure, Hirshfeld surface analysis, DFT and molecular docking studies

Douche, D., Sert, Y., Brandán, S. A., Kawther, A. A., Bilmez, B., Dege, N., Louzi, A. E., Bougrin, K., Karrouchi, K., & Himmi, B. (2021) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2021.130005 · Cited by 103

Simeprevir Potently Suppresses SARS-CoV‑2 Replication and Synergizes with Remdesivir

Lo, H. S., Hui, K. P. Y., Lai, H. M., He, X., Khan, K. S., Kaur, S., Huang, J., Li, Z., Chan, A., Cheung, H. H.-Y., et al. (2021) · ACS Central Science · doi:10.1021/acscentsci.0c01186 · Cited by 104

Tomatidine and Patchouli Alcohol as Inhibitors of SARS-CoV-2 Enzymes (3CLpro, PLpro and NSP15) by Molecular Docking and Molecular Dynamics Simulations

Zrieq, R. M., Ahmad, I., Snoussi, M., Noumi, E., Iriti, M., Algahtani, F. D., Patel, H., Saeed, M., Tasleem, M., Sulaiman, S., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221910693 · Cited by 103

Haste makes waste: A critical review of docking‐based virtual screening in drug repurposing for SARS‐CoV‐2 main protease (M‐pro) inhibition

Macip, G., Garcia‐Segura, P., Mestres‐Truyol, J., Saldivar‐Espinoza, B., Ojeda, M. J., Gimeno, A., Cereto‐Massagué, A., Garcı́a-Vallvé, S., & Pujadas, G. (2021) · Medicinal Research Reviews · doi:10.1002/med.21862 · Cited by 108

Novel thiophene Chalcones-Coumarin as acetylcholinesterase inhibitors: Design, synthesis, biological evaluation, molecular docking, ADMET prediction and molecular dynamics simulation

Hasan, A. H., Murugesan, S., Amran, S. I., Chander, S., Alanazi, M. M., Hadda, T. B., Shakya, S., Pratama, M. R. F., Das, B., Biswas, S., et al. (2021) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2021.105572 · Cited by 104

Glycosides from Buyang Huanwu Decoction inhibit atherosclerotic inflammation via JAK/STAT signaling pathway

Fu, X., Sun, Z., Long, Q., Tan, W., Ding, H., Liu, X., Wu, L., Wang, Y., & Zhang, W. (2022) · Phytomedicine · doi:10.1016/j.phymed.2022.154385 · Cited by 103

ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling

Zhang, O., Zhang, J., Jin, J., Zhang, X., Hu, R., Shen, C., Cao, H., Du, H., Kang, Y., Deng, Y., et al. (2023) · Nature Machine Intelligence · doi:10.1038/s42256-023-00712-7 · Cited by 103

An Integrated Study of Tyrosinase Inhibition by Rutin: Progress using a Computational Simulation

Si, Y.-X., Yin, S., Oh, S. H., Wang, Z., Ye, S., Li, Y., Yang, J., Park, Y., Lee, J., & Qian, G.-Y. (2012) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/073911012010525028 · Cited by 103

Demethylase Inhibitor Fungicide Resistance in Pyrenophora teres f. sp. teres Associated with Target Site Modification and Inducible Overexpression of Cyp51

Mair, W. J., Deng, W., Mullins, J. G. L., West, S., Wang, P., Besharat, N., Ellwood, S. R., Oliver, R. P., & López-Ruiz, F. J. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01279 · Cited by 102

Design, synthesis, and AChE inhibitory activity of new benzothiazole–piperazines

Özkay, Ü. D., Can, Ö. D., Sağlık, B. N., Çevik, U. A., Levent, S., Özkay, Y., Ilgın, S., & Atlı, Ö. (2016) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2016.10.041 · Cited by 102

Molecular interactions and inhibition of the staphylococcal biofilm-forming protein SdrC

Feuillie, C., Formosa‐Dague, C., Hays, L. M. C., Vervaeck, O., Derclaye, S., Brennan, M., Foster, T. J., Geoghegan, J. A., & Dufrêne, Y. F. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1616805114 · Cited by 102

Phenolic Compounds in Antimicrobial Therapy

Mandal, S. M., Dias, R. O., & Franco, O. L. (2017) · Journal of Medicinal Food · doi:10.1089/jmf.2017.0017 · Cited by 102

Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii

Ahmad, S., Raza, S., Uddin, R., & Azam, S. S. (2017) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2017.07.024 · Cited by 104

C16-ceramide is a natural regulatory ligand of p53 in cellular stress response

Fekry, B., Jeffries, K. A., Esmaeilniakooshkghazi, A., Szulc, Z. M., Knagge, K. J., Kirchner, D. R., Horita, D. A., Krupenko, S. A., & Krupenko, N. I. (2018) · Nature Communications · doi:10.1038/s41467-018-06650-y · Cited by 103

Promiscuous enzymatic activity-aided multiple-pathway network design for metabolic flux rearrangement in hydroxytyrosol biosynthesis

Chen, W., Yao, J., Meng, J., Han, W., Tao, Y., Chen, Y., Guo, Y., Shi, G., He, Y., Jin, J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08781-2 · Cited by 102

Synthesis, spectral properties, chemical descriptors and light harvesting studies of a new bioactive azo imidazole compound

Kumar, V. S., Mary, Y. S., Pradhan, K., Brahman, D., Mary, Y. S., Thomas, R., Roxy, M. S., & Alsenoy, C. V. (2019) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2019.127035 · Cited by 102

Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus

Liu, S., Zheng, Q., & Wang, Z. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa224 · Cited by 100

Anti-Inflammatory Activity and ROS Regulation Effect of Sinapaldehyde in LPS-Stimulated RAW 264.7 Macrophages

Baek, S., Park, T., Kang, M.-G., & Park, D. (2020) · Molecules · doi:10.3390/molecules25184089 · Cited by 103

Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila

Trastoy, B., Naegeli, A., Anso, I., Sjögren, J., & Guerin, M. E. (2020) · Nature Communications · doi:10.1038/s41467-020-18696-y · Cited by 104

In silico docking analysis revealed the potential of phytochemicals present in Phyllanthus amarus and Andrographis paniculata, used in Ayurveda medicine in inhibiting SARS-CoV-2

Hiremath, S. S., Kumar, H. D. V., Nandan, M., Mantesh, M., Shankarappa, K. S., Venkataravanappa, V., Basha, C. R. J., & Reddy, C. N. L. (2021) · 3 Biotech · doi:10.1007/s13205-020-02578-7 · Cited by 105

Protein engineering of stable IsPETase for PET plastic degradation by Premuse

Meng, X., Yang, L., Liu, H., Li, Q., Xu, G., Zhang, Y., Guan, F., Zhang, Y., Zhang, W., Wu, N., et al. (2021) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2021.03.058 · Cited by 103

Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro

Ngô, S. T., Tâm, N. M., Quân, P. M., & Nguyen, T. H. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00159 · Cited by 101

Drug Discovery for Mycobacterium tuberculosis Using Structure-Based Computer-Aided Drug Design Approach

Ejalonibu, M. A., Ogundare, S. A., El-Rashedy, A. A. E., Ejalonibu, M. A., Lawal, M. M., Mhlongo, N. N., & Kumalo, H. M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222413259 · Cited by 110

Antimalarial potential of naphthalene-sulfonic acid derivatives: Molecular electronic properties, vibrational assignments, and in-silico molecular docking studies

Benjamin, I., Udoikono, A. D., Louis, H., Agwamba, E. C., Unimuke, T. O., Owen, A. E., & Adeyinka, A. S. (2022) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2022.133298 · Cited by 102

Near‐Infrared Aggregation‐Induced Emission Luminogens for In Vivo Theranostics of Alzheimer's Disease

Zhang, T., Chen, X., Yuan, C., Pang, X., Shangguan, P., Liu, Y., Han, L., Sun, J., Lam, J. W. Y., Liu, Y., et al. (2022) · Angewandte Chemie International Edition · doi:10.1002/anie.202211550 · Cited by 102

Structure of human drug transporters OATP1B1 and OATP1B3

Ciută, A.-D., Nosol, K., Kowal, J., Mukherjee, S., Ramίrez, A. S., Stieger, B., Kossiakoff, A. A., & Locher, K. P. (2023) · Nature Communications · doi:10.1038/s41467-023-41552-8 · Cited by 102

Synthesis, kinetic mechanism and docking studies of vanillin derivatives as inhibitors of mushroom tyrosinase

Ashraf, Z., Rafiq, M., Seo, S., Babar, M. M., & Zaidi, N. S. (2015) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2015.06.068 · Cited by 102

Support Vector Regression Scoring of Receptor–Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries

Li, L., Wang, B., & Meroueh, S. O. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200078f · Cited by 105

Discovery of novel hybrids of diaryl-1,2,4-triazoles and caffeic acid as dual inhibitors of cyclooxygenase-2 and 5-lipoxygenase for cancer therapy

Cai, H., Huang, X., Xu, S., Shen, H., Zhang, P., Huang, Y., Jiang, J., Sun, Y., Jiang, B., Wu, X., et al. (2015) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2015.11.013 · Cited by 102

Structure-guided development of heterodimer-selective GPCR ligands

Hübner, H., Schellhorn, T., Gienger, M., Schaab, C., Kaindl, J. M., Leeb, L., Clark, T., Weikert, D., & Gmeiner, P. (2016) · Nature Communications · doi:10.1038/ncomms12298 · Cited by 102

Link-INVENT: Generative Linker Design with Reinforcement Learning

Guo, J., Knuth, F., Margreitter, C., Janet, J. P., Papadopoulos, K., Engkvist, O., & Patronov, A. (2022) · doi:10.26434/chemrxiv-2022-qkx9f · Cited by 101

Inhibition of hypoxia-inducible factor 1 with acriflavine sensitizes hypoxic tumor cells to photodynamic therapy with zinc phthalocyanine-encapsulating cationic liposomes

Broekgaarden, M., Weijer, R., Krekorian, M., van den IJssel, B., Kos, M., Alles, L. K., van Wijk, A. C. W. A., Bikádi, Z., Hazai, E., van Gulik, T. M., et al. (2016) · Nano Research · doi:10.1007/s12274-016-1059-0 · Cited by 101

Synthesis, structural, DFT studies, docking and antibacterial activity of a xanthene based hydrazone ligand

Naseem, S., Khalid, M., Tahir, M. N., Halim, M. A., Braga, A. A. C., Naseer, M. M., & Shafiq, Z. (2017) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2017.04.093 · Cited by 101

Imiquimod-induced psoriasis-like inflammation in differentiated Human keratinocytes: Its evaluation using curcumin

Varma, S. R., Sivaprakasam, T. O., Mishra, A., Prabhu, S. V., Rafiq, M., & Paramesh, R. (2017) · European Journal of Pharmacology · doi:10.1016/j.ejphar.2017.07.040 · Cited by 101

Regulation of the Hippo Pathway by Phosphatidic Acid-Mediated Lipid-Protein Interaction

Han, H., Qi, R., Zhou, J. J., TA, A., Yang, B., Nakaoka, H. J., Seo, G., Guan, K., Luo, R., & Wang, W. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.08.038 · Cited by 99

A synthetic microbial biosensor for high-throughput screening of lactam biocatalysts

Yeom, S., Kim, M., Kwon, K. K., Fu, Y., Rha, E., Park, S. H., Lee, H., Kim, H., Lee, D., Kim, D., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07488-0 · Cited by 102

Multiple functional neurosteroid binding sites on GABAA receptors

Chen, Z.-W., Bracamontes, J. R., Budelier, M. M., Germann, A. L., Shin, D. J., Krishnan, K., Qian, M., Manion, B. D., Cheng, W. W. L., Reichert, D. E. C., et al. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000157 · Cited by 102

High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2

Strodel, B., Olubiyi, O. O., Olagunju, M. O., Keutmann, M., & Loschwitz, J. (2020) · Molecules · doi:10.3390/molecules25143193 · Cited by 100

Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies

Batra, R., Chan, H., Kamath, G., Ramprasad, R., Cherukara, M. J., & Sankaranarayanan, S. K. R. S. (2020) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.0c02278 · Cited by 106

SuperNatural 3.0—a database of natural products and natural product-based derivatives

Gallo, K., Kemmler, E., Goede, A., Becker, F., Dunkel, M., Preißner, R., & Banerjee, P. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1008 · Cited by 101

Investigate the Binding of Catechins to Trypsin Using Docking and Molecular Dynamics Simulation

Cui, F., Yang, K., & Li, Y. (2015) · PLoS ONE · doi:10.1371/journal.pone.0125848 · Cited by 101

Molecular Mechanism and Evolution of Guanylate Kinase Regulation by (p)ppGpp

Liu, K., Myers, A. R., Pisithkul, T., Claas, K. R., Satyshur, K. A., Amador‐Noguez, D., Keck, J. L., & Wang, J. D. (2015) · Molecular Cell · doi:10.1016/j.molcel.2014.12.037 · Cited by 102

Interaction prediction in structure-based virtual screening using deep learning

Gonczarek, A., Tomczak, J. M., Zaręba, S., Kaczmar-Michalska, J., Dąbrowski, P., & Walczak, M. (2017) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2017.09.007 · Cited by 105

Small Molecule Enhancement of 20S Proteasome Activity Targets Intrinsically Disordered Proteins

Jones, C. L., Njomen, E., Sjögren, B., Dexheimer, T. S., & Tepe, J. J. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00489 · Cited by 100

Molecular Aspects of core-shell Intrinsic Defect Induced Enhanced Antibacterial Activity of ZnO Nanocrystals

Verma, S. K., Jha, E., Panda, P. K., Das, J. K., Thirumurugan, A., Suar, M., & Parashar, S. (2017) · Nanomedicine · doi:10.2217/nnm-2017-0237 · Cited by 100

Chlorogenic acid attenuates virulence factors and pathogenicity of Pseudomonas aeruginosa by regulating quorum sensing

Wang, H., Chu, W., Ye, C., Gaëta, B. A., Tao, H., Wang, M., & Qiu, Z. (2018) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-018-9482-7 · Cited by 100

Generation of amine dehydrogenases with increased catalytic performance and substrate scope from ε-deaminating L-Lysine dehydrogenase

Tseliou, V., Knaus, T., Masman, M. F., Corrado, M. L., & Mutti, F. G. (2019) · Nature Communications · doi:10.1038/s41467-019-11509-x · Cited by 100

The citrus flavonoid naringenin impairs the in vitro infection of human cells by Zika virus

Cataneo, A. H. D., Kuczera, D., Koishi, A. C., Zanluca, C., Silveira, G. F., de Arruda, T. B., Suzukawa, A. A., Bortot, L. O., Dias‐Baruffi, M., Verri, W. A., Jr., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-52626-3 · Cited by 102

Developing a highly efficient hydroxytyrosol whole-cell catalyst by de-bottlenecking rate-limiting steps

Yao, J., He, Y., Su, N., Bharath, S. R., Tao, Y., Jin, J., Chen, W., Song, H., & Tang, S. (2020) · Nature Communications · doi:10.1038/s41467-020-14918-5 · Cited by 100

A network pharmacology approach to investigate the mechanism of Shuxuening injection in the treatment of ischemic stroke

Cui, Q., Zhang, Y.-L., Ma, Y., Yu, H., Zhao, X.-Z., Zhang, L., Ge, S., Zhang, G., & Qin, X. (2020) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2020.112891 · Cited by 103

Identification of high-affinity inhibitors of SARS-CoV-2 main protease: Towards the development of effective COVID-19 therapy

Mohammad, T., Shamsi, A., Anwar, S., Umair, M., Hussain, A., Rehman, M. T., Alajmi, M. F., Islam, A., & Hassan, M. I. (2020) · Virus Research · doi:10.1016/j.virusres.2020.198102 · Cited by 100

Active-site loop variations adjust activity and selectivity of the cumene dioxygenase

Heinemann, P. M., Armbruster, D., & Hauer, B. (2021) · Nature Communications · doi:10.1038/s41467-021-21328-8 · Cited by 99

Versatility in acyltransferase activity completes chicoric acid biosynthesis in purple coneflower

Fu, R., Zhang, P., Jin, G., Wang, L., Qi, S., Cao, Y., Martin, C. R., & Zhang, Y. (2021) · Nature Communications · doi:10.1038/s41467-021-21853-6 · Cited by 100

Structural requirements of flavonoids for the selective inhibition of α-amylase versus α-glucosidase

Lim, J., Ferruzzi, M. G., & Hamaker, B. R. (2021) · Food Chemistry · doi:10.1016/j.foodchem.2021.130981 · Cited by 100

Structural Insights into (Tere)phthalate-Ester Hydrolysis by a Carboxylesterase and Its Role in Promoting PET Depolymerization

von Haugwitz, G., Han, X., Pfaff, L., Li, Q., Wei, H., Gao, J., Methling, K., Ao, Y., Brack, Y., Mičan, J., et al. (2022) · ACS Catalysis · doi:10.1021/acscatal.2c03772 · Cited by 100

The Impact of Software Used and the Type of Target Protein on Molecular Docking Accuracy

Ivanova, L. B., & Karelson, M. M. (2022) · Molecules · doi:10.3390/molecules27249041 · Cited by 112

Comprehensive Survey of Consensus Docking for High-Throughput Virtual Screening

Blanes‐Mira, C., Fernández-Aguado, P., de Andrés-López, J., Fernández-Carvajal, A. M., Ferrer-Montiel, A. V., & Fernandez-Ballester, G. J. (2022) · Molecules · doi:10.3390/molecules28010175 · Cited by 113

A practical guide to machine-learning scoring for structure-based virtual screening

Tran‐Nguyen, V., Junaid, M., Simeon, S., & Ballester, P. J. (2023) · Nature Protocols · doi:10.1038/s41596-023-00885-w · Cited by 106

Illustrated Procedure to Perform Molecular Docking Using PyRx and Biovia Discovery Studio Visualizer: A Case Study of 10kt With Atropine

Ayodele, P. F., Bamigbade, A. T., Bamigbade, O. O., Adeniyi, I. A., Tachin, E. S., Seweje, A. J., & Farohunbi, S. T. (2023) · Progress in Drug Discovery & Biomedical Science · doi:10.36877/pddbs.a0000424 · Cited by 100

Blockade of PI3K/AKT signaling pathway by Astragaloside IV attenuates ulcerative colitis via improving the intestinal epithelial barrier

Zhang, X., Zhang, F., Li, Y., Fan, N., Zhao, K., Zhang, A., Kang, J., Yan, L., Xue, X., & Jiang, X. (2024) · Journal of Translational Medicine · doi:10.1186/s12967-024-05168-w · Cited by 100

The molecular basis for Mucosal-Associated Invariant T cell recognition of MR1 proteins

López‐Sagaseta, J., Dulberger, C. L., Crooks, J. E., Parks, C. D., Luoma, A., McFedries, A., Rhijn, I. V., Saghatelian, A., & Adams, E. J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1222678110 · Cited by 103

RELATION: A Deep Generative Model for Structure-Based De Novo Drug Design

Wang, M., Hsieh, C.-Y., Wang, J., Wang, D., Weng, G., Shen, C., Yao, X., Bing, Z., Li, H., Cao, D., et al. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.2c00732 · Cited by 99

Indolinone-based acetylcholinesterase inhibitors: Synthesis, biological activity and molecular modeling

Akrami, H., Mirjalili, B. F., Khoobi, M., Nadri, H., Moradi, A., Sakhteman, A., Emami, S., Foroumadi, A., & Shafiee, A. (2014) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2014.01.017 · Cited by 99

Pyoverdine, the Major Siderophore inPseudomonas aeruginosa, Evades NGAL Recognition

Peek, M. E., Bhatnagar, A., McCarty, N. A., & Zughaier, S. M. (2012) · Interdisciplinary Perspectives on Infectious Diseases · doi:10.1155/2012/843509 · Cited by 104

Propargylamine as Functional Moiety in the Design of Multifunctional Drugs for Neurodegenerative Disorders: MAO Inhibition and Beyond

Zindo, F. T., Joubert, J., & Malan, S. F. (2015) · Future Medicinal Chemistry · doi:10.4155/fmc.15.12 · Cited by 99

Compensation by the E138K Mutation in HIV-1 Reverse Transcriptase for Deficits in Viral Replication Capacity and Enzyme Processivity Associated with the M184I/V Mutations

Xu, H., Asahchop, E. L., Oliveira, M., Quashie, P. K., Quan, Y., BRENNER, B. G., & Wainberg, M. A. (2011) · Journal of Virology · doi:10.1128/jvi.05584-11 · Cited by 99

Improvement in Thermal Stability of Sucralose by γ-Cyclodextrin Metal-Organic Frameworks

Lv, N., Guo, T., Liu, B., Wang, C., Singh, V., Xu, X., Li, X., Chen, D., Gref, R., & Zhang, J. (2016) · Pharmaceutical Research · doi:10.1007/s11095-016-2059-1 · Cited by 99

Deep convolutional networks for quality assessment of protein folds

Derevyanko, G., Grudinin, S., Bengio, Y., & Lamoureux, G. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty494 · Cited by 103

Design and development of Isatin-triazole hydrazones as potential inhibitors of microtubule affinity-regulating kinase 4 for the therapeutic management of cell proliferation and metastasis

Aneja, B., Khan, N. S., Κhan, P., Queen, A., Hussain, A., Rehman, M. T., Alajmi, M. F., El-Seedi, H. R., Ali, S., Hassan, M. I., et al. (2018) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2018.12.026 · Cited by 100

Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

Evoli, S., Mobley, D. L., Guzzi, R., & Rizzuti, B. (2016) · Physical Chemistry Chemical Physics · doi:10.1039/c6cp05680f · Cited by 103

Molecular basis of PIP2-dependent regulation of the Ca2+-activated chloride channel TMEM16A

Le, S. C., Jia, Z., Chen, J., & Yang, H. (2019) · Nature Communications · doi:10.1038/s41467-019-11784-8 · Cited by 100

Screening of different drug design tools to predict the mode of action of steroidal derivatives as anti-cancer agents

Nafie, M. S., Tantawy, M. A., & Elmegeed, G. A. (2019) · Steroids · doi:10.1016/j.steroids.2019.108485 · Cited by 99

Perfluorooctanoic acid alters progesterone activity in human endometrial cells and induces reproductive alterations in young women

Nisio, A. D., Rocca, M. S., Šabović, I., Ponce, M. D. R., Corsini, C., Guidolin, D., Zanon, C., Acquasaliente, L., Carosso, A. R., Toni, L. D., et al. (2019) · Chemosphere · doi:10.1016/j.chemosphere.2019.125208 · Cited by 103

Synthesis, DFT, computational exploration of chemical reactivity, molecular docking studies of novel formazan metal complexes and their biological applications

Khan, S. A., Rızwan, K., Shahid, S., Noamaan, M. A., Rasheed, T., & Amjad, H. (2020) · Applied Organometallic Chemistry · doi:10.1002/aoc.5444 · Cited by 99

Promising terpenes as SARS-CoV-2 spike receptor-binding domain (RBD) attachment inhibitors to the human ACE2 receptor: Integrated computational approach

Muhseen, Z. T., Hameed, A. R., Al-Hasani, H. M. H., Qamar, M. T. U., & Li, G. (2020) · Journal of Molecular Liquids · doi:10.1016/j.molliq.2020.114493 · Cited by 100

HO‐1 Contributes to Luteolin‐Triggered Ferroptosis in Clear Cell Renal Cell Carcinoma via Increasing the Labile Iron Pool and Promoting Lipid Peroxidation

Han, S., Lin, F., Qi, Y., Liu, C., Zhou, L., Xia, Y., Chen, K., Ji, X., Li, H., Yu, W., et al. (2022) · Oxidative Medicine and Cellular Longevity · doi:10.1155/2022/3846217 · Cited by 101

Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina

Agarwal, R., & Smith, J. C. (2022) · Molecular Informatics · doi:10.1002/minf.202200188 · Cited by 109

Computational drug repurposing: approaches, evaluation of in silico resources and case studies

Tanoli, Z., Fernández‐Torras, A., Özcan, U. O., Kushnir, A., Nader, K. M., Gadiya, Y., Fiorenza, L., Ianevski, A., Vähä-Koskela, M. J. V., Miihkinen, M., et al. (2025) · Nature Reviews Drug Discovery · doi:10.1038/s41573-025-01164-x · Cited by 104

1 Structural bioinformatics Fast, Accurate, and Reliable Molecular Docking with QuickVina 2

Alhossary, A., Handoko, S. D., & Mu, Y. (2016)

Fast, accurate, and reliable molecular docking with QuickVina 2

Alhossary, A., Handoko, S. D., Mu, Y., & Kwoh, C. K. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv082 · Cited by 399

QuickVina: Accelerating AutoDock Vina Using Gradient-Based Heuristics for Global Optimization

Handoko, S. D., Ouyang, X., Su, C. T.-T., Kwoh, C. K., & Ong, Y.-S. (2012) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2012.82 · Cited by 69

Accelerating AutoDock Vina with GPUs

Tang, S., Chen, R., Mengru, L., Qingde, L., Zhu, Y., Ding, J., Wu, J., Haifeng, H., & Ming, L. (2022) · Molecules · doi:10.3390/molecules27093041 · Cited by 134

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

Eberhardt, J., Santos‐Martins, D., Tillack, A. F., & Forli, S. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00203 · Cited by 8,292