A semiempirical free energy force field with charge‐based desolvation

A new force field for molecular mechanical simulation of nucleic acids and proteins

Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., & Weiner, P. K. (1984) · Journal of the American Chemical Society · doi:10.1021/ja00315a051 · Cited by 4,641

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

Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges

Gasteiger, J., & Marsili, M. (1980) · Tetrahedron · doi:10.1016/0040-4020(80)80168-2 · Cited by 4,157

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

Virtual Computational Chemistry Laboratory – Design and Description

Tetko, I. V., Gasteiger, J., Todeschini, R., Mauri, A., Livingstone, D. J., Ertl, P., Palyulin, V. A., Radchenko, E. V., Zefirov, N. S., Makarenko, A. S., et al. (2005) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-005-8694-y · Cited by 1,504

Principles of docking: An overview of search algorithms and a guide to scoring functions

Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294

Protein–ligand docking: Current status and future challenges

Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21082 · Cited by 1,047

Molecular Recognition and Docking Algorithms

Brooijmans, N., & Kuntz, I. D. (2003) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.142532 · Cited by 812

A review of protein-small molecule docking methods

Taylor, R. D., Jewsbury, P. J., & Essex, J. W. (2002) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1020155510718 · Cited by 685

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

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

The cardenolides strophanthidin, digoxigenin and dihydroouabain act as activators of the human RORγ/RORγT receptors

Karaś, K., Sałkowska, A., Walczak‐Drzewiecka, A., Ryba, K., Dastych, J., Bachorz, R. A., & Ratajewski, M. (2018) · Toxicology Letters · doi:10.1016/j.toxlet.2018.07.002 · Cited by 27

Porous β-cyclodextrin nanotubular assemblies enable high-efficiency removal of bisphenol micropollutants from aquatic systems

He, W., Ren, X., Yan, Z., Wang, J., & Lu, L. (2020) · Nano Research · doi:10.1007/s12274-020-2758-0 · Cited by 27

Synthesis, Characterization, Antimicrobial Evaluation, and Computational Investigation of Substituted Imidazo[2,1‐ b ][1,3,4]Thiadiazole Derivatives

Dagli, M., Er, M., Karakurt, T., Onaran, A., Alıcı, H., & Tahtacı, H. (2020) · ChemistrySelect · doi:10.1002/slct.202002821 · Cited by 27

Molecular docking study of flavonoid compounds for possible matrix metalloproteinase-13 inhibition

Taherkhani, A., Moradkhani, S., Orangi, A., Jalalvand, A., & Khamverdi, Z. (2020) · Journal of Basic and Clinical Physiology and Pharmacology · doi:10.1515/jbcpp-2020-0036 · Cited by 27

Membrane Vesicles for Nanoencapsulated Sulforaphane Increased Their Anti-Inflammatory Role on an In Vitro Human Macrophage Model

Yepes‐Molina, L., Pérez-Jiménez, M. I., Martinez‐Esparza, M., Teruel, J. A., Ruiz‐Alcaraz, A. J., García–Peñarrubia, P., & Carvajal, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23041940 · Cited by 27

Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints

Fujimoto, K. J., Minami, S., & Yanai, T. (2022) · ACS Omega · doi:10.1021/acsomega.2c02822 · Cited by 29

Thiadiazole Functionalized Salicylaldehyde-Schiff Base as a pH-responsive and chemo-reversible “Turn-Off” fluorescent probe for selective cu (II) detection: Logic Gate Behaviour and Molecular Docking Studies

Chhikara, A., Tomar, D., Bartwal, G., Chaurasia, M., Sharma, A., Gopal, S., & Chandra, S. (2022) · Journal of Fluorescence · doi:10.1007/s10895-022-02991-6 · Cited by 27

The fibrate gemfibrozil is a NO ‐ and haem‐independent activator of soluble guanylyl cyclase : in vitro studies

Sharina, I. G., Sobolevsky, M., Papakyriakou, A., Rukoyatkina, N., Spyroulias, G. A., Gambaryan, S. P., & Martin, E. (2014) · British Journal of Pharmacology · doi:10.1111/bph.13055 · Cited by 28

Synthesis, characterization and urease inhibitory activity of oxovanadium(V) complexes with similar Schiff bases

You, Z., Cui, Y., Ma, Y.-P., Wang, C., Zhou, X., & Li, K. (2011) · Inorganic Chemistry Communications · doi:10.1016/j.inoche.2011.01.038 · Cited by 27

Computer-aided de novo ligand design and docking/molecular dynamics study of Vitamin D receptor agonists

Shen, X., Takimoto‐Kamimura, M., Wei, J., & Gao, Q. (2011) · Journal of Molecular Modeling · doi:10.1007/s00894-011-1066-8 · Cited by 27

Molecular modeling of the alpha9alpha10 nicotinic acetylcholine receptor subtype.

Pérez, E. G., Cassels, B., & Zapata-Torres, G. (2009) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2008.10.094 · Cited by 25

A Potential Substrate Binding Conformation of β-Lactams and Insight into the Broad Spectrum of NDM-1 Activity

Yuan, Q., He, L. S., & Ke, H. (2012) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.05896-11 · Cited by 27

(+)-Ascosalitoxin and Vermelhotin, a Calmodulin Inhibitor, from an Endophytic Fungus Isolated from Hintonia latiflora

Leyte‐Lugo, M., González‐Andrade, M., González, M. D. C., Glenn, A. E., Cerda-García-Rojas, C. M., & Mata, R. (2012) · Journal of Natural Products · doi:10.1021/np300327y · Cited by 27

Synthesis and structure–activity relationships of novel hybrid ferrocenyl compounds based on a bicyclic core skeleton for breast cancer therapy

Li, C., Tang, C. C., Hu, Z., Zhao, C., Li, C., Zhang, S., Dong, C., Zhou, H., & Huang, J. (2016) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2016.05.019 · Cited by 27

Mutagenesis of α-Conotoxins for Enhancing Activity and Selectivity for Nicotinic Acetylcholine Receptors

Turner, M. W., Marquart, L. A., Phillips, P. D., & McDougal, O. M. (2019) · Toxins · doi:10.3390/toxins11020113 · Cited by 28

Microwave and conventional synthesis of ester based dicationic pyridinium ionic liquids carrying hydrazone linkage: DNA binding, anticancer and docking studies

Al-Sodies, S., Aouad, M. R., Ihmaid, S. K., Aljuhani, A., Messali, M., Ali, I., & Rezki, N. (2020) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2020.127756 · Cited by 27

Activation of Nucleotide-Binding Oligomerization Domain 1 (NOD1) Receptor Signaling in Labeo rohita by iE-DAP and Identification of Ligand-Binding Key Motifs in NOD1 by Molecular Modeling and Docking

Sahoo, B. R., Swain, B., Dikhit, M. R., Basu, M., Bej, A., Jayasankar, P., & Samanta, M. (2013) · Applied Biochemistry and Biotechnology · doi:10.1007/s12010-013-0263-6 · Cited by 25

Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking

Guan, B., Zhang, C., & Ning, J. (2017) · AMB Express · doi:10.1186/s13568-017-0476-0 · Cited by 26

Total Synthesis of Pulmonarin B and Design of Brominated Phenylacetic Acid/Tacrine Hybrids: Marine Pharmacophore Inspired Discovery of New ChE and Aβ Aggregation Inhibitors

Cheng, Z., Song, J.-L., Zhu, K., Zhang, J., Jiang, C., & Zhang, H. (2018) · Marine Drugs · doi:10.3390/md16090293 · Cited by 26

Urea and thiourea derivatives of 3-(trifluoromethyl)-5,6,7,8-tetrahydro-[1, 2, 4]triazolo[4,3-a]pyrazine: Synthesis, characterization, antimicrobial activity and docking studies

Mannam, M. R., Devineni, S. R., Pavuluri, C. M., Raju, C. N., & Kottapalli, R. P. (2019) · Phosphorus, sulfur, and silicon and the related elements · doi:10.1080/10426507.2019.1577845 · Cited by 26

3,4-Dibromo-7-Azaindole Modulates Arabidopsis Circadian Clock by Inhibiting Casein Kinase 1 Activity

Ono, A., Sato, A., Fujimoto, K. J., Matsuo, H., Yanai, T., Kinoshita, T., & Nakamichi, N. (2019) · Plant and Cell Physiology · doi:10.1093/pcp/pcz183 · Cited by 26

Novel insights into oxidation of fatty acids and fatty alcohols by cytochrome P450 monooxygenase CYP4B1

Theßeling, F. A., Hutter, M. C., Wiek, C., Kowalski, J. P., Rettie, A. E., & Girhard, M. (2019) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2019.108216 · Cited by 25

Benzimidazole and Benzoxazole Zinc Chelators as Inhibitors of Metallo‐β‐Lactamase NDM‐1

Jackson, A. C., Pinter, T. B. J., Talley, D. C., Baker‐Agha, A., Patel, D., Smith, P. J., & Franz, K. J. (2020) · ChemMedChem · doi:10.1002/cmdc.202000607 · Cited by 26

High-throughput screening of natural compounds and inhibition of a major therapeutic target HsGSK-3β for Alzheimer’s disease using computational approaches

Shukla, R., & Singh, T. R. (2021) · Journal of Genetic Engineering and Biotechnology · doi:10.1186/s43141-021-00163-w · Cited by 26

Design and various in silico studies of the novel curcumin derivatives as potential candidates against COVID-19 -associated main enzymes

Alıcı, H., Tahtacı, H., & Demır, K. (2022) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2022.107657 · Cited by 28

Discovery of Novel α-Aminophosphonates with Hydrazone as Potential Antiviral Agents Combined With Active Fragment and Molecular Docking

Jia, T., Ji, R., Wang, H., Li, S., & Zhang, G. (2022) · Frontiers in Chemistry · doi:10.3389/fchem.2022.911453 · Cited by 26

Mechanistic insights into the mitigation of Aβ aggregation and protofibril destabilization by a d -enantiomeric decapeptide rk10

Singh, K., Kaur, A., Goyal, D., & Goyal, B. (2022) · Physical Chemistry Chemical Physics · doi:10.1039/d2cp02601e · Cited by 26

Insilico generation of novel ligands for the inhibition of SARS-CoV-2 main protease (3CLpro) using deep learning

Prabhakaran, P., Hebbani, A. V., Menon, S. V., Paital, B., Murmu, S., Kumar, S., Singh, M. K., Sahoo, D. K., & Desai, P. P. D. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1194794 · Cited by 26

Development of novel small peptide ligands for antibody purification

Wei, Y., Xu, J., Zhang, L., Fu, Y., & Xu, X. (2015) · RSC Advances · doi:10.1039/c5ra07829f · Cited by 26

Three-dimensional models of 14α-sterol demethylase (Cyp51A) from Aspergillus lentulus and Aspergillus fumigatus: an insight into differences in voriconazole interaction

Alcázar‐Fuoli, L., Cuesta, I., Rodrı́guez-Tudela, J. L., Cuenca‐Estrella, M., Sanglard, D., & Mellado, E. (2011) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2011.06.005 · Cited by 26

Paramagnetic Nuclear Magnetic Resonance Relaxation and Molecular Mechanics Studies of the Chloroperoxidase–Indole Complex: Insights into the Mechanism of Chloroperoxidase-Catalyzed Regioselective Oxidation of Indole

Zhang, R., He, Q., Chatfield, D. C., & Wang, X. (2013) · Biochemistry · doi:10.1021/bi4002437 · Cited by 26

Synthesis, in vitro and in silico screening of ethyl 2-(6-substituted benzo[d]thiazol-2-ylamino)-2-oxoacetates as protein-tyrosine phosphatase 1B inhibitors

Navarrete‐Vázquez, G., Ramírez-Martínez, M., Estrada-Soto, S. E., Nava-Zuazo, C., Paoli, P., Camici, G., Escalante, J., Medina‐Franco, J. L., López-Vallejo, F., & Ortíz‐Andrade, R. (2012) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2012.04.025 · Cited by 26

New Insight into the Binding Mode of Peptide Ligands at Urotensin-II Receptor: Structure−Activity Relationships Study on P5U and Urantide

Grieco, P., Carotenuto, A., Campiglia, P., Gomez-Monterrey, I. M., Auriemma, L., Sala, M., Marcozzi, C., Bianca, R. D. D. V., Brancaccio, D., Rovero, P., et al. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm900148c · Cited by 26

Synthesis, molecular docking, and activity of Schiff-base copper(II) complex with N-n-butylsalicylaldiminate as Helicobacter pylori urease inhibitor

Cui, Y. M., Li, Y., Cai, Y., Chen, W., & Zhu, H. (2011) · Journal of Coordination Chemistry · doi:10.1080/00958972.2011.552110 · Cited by 26

Substrate-mediated Fidelity Mechanism Ensures Accurate Decoding of Proline Codons

So, B. R., An, S., Kumar, S., Das, M., Turner, D. A., Hadad, C. M., & Musier‐Forsyth, K. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.232611 · Cited by 26

The structures, cytotoxicity, apoptosis and molecular docking controlled by the aliphatic chain of palladium(II) complexes

Zhu, M., Cui, X., Zhang, S., Liu, L., Han, Z., & Gao, E. (2016) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2016.01.016 · Cited by 26

Docking, Synthesis and Evaluation of Antioxidant Activity of 2,4,5-Triaryl Imidazole

Singh, P., & Kumar, R. (2015) · Clinical & Medical Biochemistry Open Access · doi:10.4172/2471-2663.1000105 · Cited by 26

Chiral HPLC Separation and Modeling of Four Stereomers of DL‐Leucine‐DL‐Tryptophan Dipeptide on Amylose Chiral Column

Alajmi, M. F., Hussain, A., Suhail, M., Mukhtar, S. D., Sahoo, D. R., Asnin, L. D., & Ali, I. (2016) · Chirality · doi:10.1002/chir.22624 · Cited by 26

Selenophenes: Introducing a New Element into the Core of Non‐Steroidal Estrogen Receptor Ligands

Zhang, S., Wang, Z., Hu, Z., Li, C., Tang, C. C., Carlson, K. E., Luo, J., Dong, C., Katzenellenbogen, J. A., Huang, J., et al. (2016) · ChemMedChem · doi:10.1002/cmdc.201600593 · Cited by 26

Design, synthesis and collagenase inhibitory activity of some novel phenylglycine derivatives as metalloproteinase inhibitors

Ganeshpurkar, A., Kumar, D., & Singh, S. K. (2017) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2017.10.008 · Cited by 26

In Silico Studies Targeting G-protein Coupled Receptors for Drug Research Against Parkinson’s Disease

Lemos, A., Melo, R., Preto, A. J., de Almeida, J. G., Moreira, I. S., & Cordeiro, M. N. D. S. (2018) · Current Neuropharmacology · doi:10.2174/1570159x16666180308161642 · Cited by 28

Potential novel inhibitors against emerging zoonotic pathogen Nipah virus: a virtual screening and molecular dynamics approach

Ropón‐Palacios, G., Zuta, M. E. C., Olivos-Ramirez, G. E., Otazu, K., Saavedra, J. A., & Camps, I. (2019) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2019.1655480 · Cited by 26

Discovery of the Novel Inhibitor Against New Delhi Metallo-β-Lactamase Based on Virtual Screening and Molecular Modelling

Wang, X., Yang, Y., Gao, Y., & Niu, X. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21103567 · Cited by 26

Synthesis, biological evaluation, and molecular modeling of 3,5-substituted-N1-phenyl-N4,N4-di-n-butylsulfanilamides as antikinetoplastid antimicrotubule agents

George, T. G., Endeshaw, M. M., Morgan, R. E., Mahasenan, K. V., Delfín, D. A., Mukherjee, M. S., Yakovich, A. J., Fotie, J., Li, C., & Werbovetz, K. A. (2007) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2007.06.042 · Cited by 26

Identification of Anxiolytic/Nonsedative Agents among Indol-3-ylglyoxylamides Acting as Functionally Selective Agonists at the γ-Aminobutyric Acid-A (GABAA) α2Benzodiazepine Receptor

Taliani, S., Cosimelli, B., Settimo, F. D., Marini, A. M., Motta, C. L., Simorini, F., Salerno, S., Novellino, E., Greco, G., Cosconati, S., et al. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm9001154 · Cited by 26

Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility

Bolia, A., & Ozkan, S. B. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00587 · Cited by 26

Molecular Docking as a Tool to Examine Organic Cation Sorption to Organic Matter

Scott, S., Fernandez, J. P., Hadad, C. M., & MacKay, A. A. (2022) · Environmental Science & Technology · doi:10.1021/acs.est.1c06147 · Cited by 25

Design, synthesis and biological evaluation of shikonin thio-glycoside derivatives: new anti-tubulin agents

Lin, H., Han, H., Bai, L., Qiu, H., Yin, D.-Z., Qi, J., Wang, X., Gu, H.-W., & Yang, Y. (2014) · RSC Advances · doi:10.1039/c4ra08810g · Cited by 25

Synthesis, characterization and urease inhibition of a novel acetylhydroxamate-coordinated oxovanadium(V) complex with hydrazone ligand

Huo, Y., Ye, Y., Cheng, X.-S., & You, Z. (2014) · Inorganic Chemistry Communications · doi:10.1016/j.inoche.2014.04.008 · Cited by 25

Fungal bis-Naphthopyrones as Inhibitors of Botulinum Neurotoxin Serotype A

Cardellina, J. H., Roxas-Duncan, V. I., Montgomery, V. A., Eccard, V. S., Campbell, Y. G., Hu, X., Khavrutskii, I. V., Tawa, G. J., Wallqvist, A., Gloer, J. B., et al. (2012) · ACS Medicinal Chemistry Letters · doi:10.1021/ml200312s · Cited by 25

Discovery of potent small molecule inhibitors of DYRK1A by structure-based virtual screening and bioassay

Wang, D., Wang, F., Tan, Y., Dong, L., Chen, L., Zhu, W., & Wang, H. (2011) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2011.11.043 · Cited by 25

MT119, a new planar‐structured compound, targets the colchicine site of tubulin arresting mitosis and inhibiting tumor cell proliferation

Zhang, Z., Meng, T., Yang, N., Wang, W., Xiong, B., Chen, Y., Ma, L., Shen, J., Miao, Z., & Ding, J. (2010) · International Journal of Cancer · doi:10.1002/ijc.25661 · Cited by 25

Modeling of Arylamide Helix Mimetics in the p53 Peptide Binding Site of hDM2 Suggests Parallel and Anti-Parallel Conformations Are Both Stable

Fuller, J. C., Jackson, R. M., Edwards, T. A., Wilson, A. J., & Shirts, M. R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043253 · Cited by 24

Design, synthesis and biological evaluation of urea derivatives from o-hydroxybenzylamines and phenylisocyanate as potential FabH inhibitors

Li, Z.-L., Li, Q., Zhang, H., Hu, Y., Zhu, D.-D., & Zhu, H. (2011) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2011.06.049 · Cited by 25

Enhanced Emission of Zinc Nitride Colloidal Nanoparticles with Organic Dyes for Optical Sensors and Imaging Application

Soundharraj, P., Durgalakshmi, D., Karthikeyan, S., Aruna, P., & Ganesan, S. (2020) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.9b21585 · Cited by 25

Synthesis, in vitro and structural aspects of benzothiazole analogs as anti-oxidants and potential neuroprotective agents

Ramaiah, M. J., Karthikeyan, D., Mathavan, S., Yamajala, R. B. R. D., Ramachandran, S., Vasavi, P. J., & Chandana, N. V. (2020) · Environmental Toxicology and Pharmacology · doi:10.1016/j.etap.2020.103415 · Cited by 25

Discovery of Dithioacetal Derivatives Containing Sulfonamide Moiety of Novel Antiviral Agents by TMV Coat Protein as a Potential Target

Yang, Y., Zhang, J., Li, X., He, F., Wu, R., Hu, D., & Song, B. (2020) · ACS Omega · doi:10.1021/acsomega.0c03306 · Cited by 25

Insights into Molecular Mechanisms of EGCG and Apigenin on Disrupting Amyloid-Beta Protofibrils Based on Molecular Dynamics Simulations

Fang, M., Zhang, Q., Guan, P., Su, K., Wang, X., & Hu, X. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04230 · Cited by 26

Oxygen mediated oxidative couplings of flavones in alkaline water

Yang, X., Lim, S. H. M., Lin, J., Wu, J., Tang, H., Zhao, F., Liu, F., Sun, C., Shi, X., Kuang, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34123-w · Cited by 25

TB-IECS: an accurate machine learning-based scoring function for virtual screening

Zhang, X., Shen, C., Jiang, D., Zhang, J., Ye, Q., Xu, L., Hou, T., Pan, P., & Kang, Y. (2023) · Journal of Cheminformatics · doi:10.1186/s13321-023-00731-x · Cited by 28

A natural heme‐signature variant of CYP 267A1 from Sorangium cellulosum So ce56 executes diverse ω‐hydroxylation

Khatri, Y., Hannemann, F., Girhard, M., Kappl, R., Hutter, M. C., Urlacher, V. B., & Bernhardt, R. (2014) · FEBS Journal · doi:10.1111/febs.13104 · 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

SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems

Strunk, T., Wolf, M., Brieg, M., Klenin, K., Biewer, A., Tristram, F., Ernst, M., Kleine, P. J., Heilmann, N., Kondov, I., et al. (2012) · Journal of Computational Chemistry · doi:10.1002/jcc.23089 · Cited by 25

Mechanism of Taq DNA Polymerase Inhibition by Fullerene Derivatives: Insight from Computer Simulations

Nedumpully-Govindan, P., Monticelli, L., & Salonen, E. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp3046577 · Cited by 25

The effect of dichlorvos on the structural alteration of serum albumins: a combined spectroscopic and molecular dynamic simulation approach

Mohammadi, T., Ghayeb, Y., Sharifi, T., & Khayamian, T. (2016) · Monatshefte für Chemie - Chemical Monthly · doi:10.1007/s00706-016-1857-9 · Cited by 25

Computer-Aided Analysis of Multiple SARS-CoV-2 Therapeutic Targets: Identification of Potent Molecules from African Medicinal Plants

Iheagwam, F. N., & Rotimi, S. O. (2020) · Scientifica · doi:10.1155/2020/1878410 · Cited by 25

Oxidation of human cytochrome P450 1A2 substrates by Bacillus megaterium cytochrome P450 BM3

Kim, D., Kim, K., Kim, D., Jung, H.-C., Pan, J., Chi, Y.-T., Ahn, T., & Yun, C. (2010) · Journal of Molecular Catalysis B Enzymatic · doi:10.1016/j.molcatb.2010.01.017 · Cited by 25

Rotamer libraries and probabilities of transition between rotamers for the side chains in protein–protein binding

Kirys, T., Ruvinsky, A. M., Tuzikov, A. V., & Vakser, I. A. (2012) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24103 · Cited by 25

A more detailed picture of the interactions between virtual screening-derived hits and the DNA G-quadruplex: NMR, molecular modelling and ITC studies

Trotta, R., Tito, S. D., Lauri, I., Pietra, V. L., Marinelli, L., Cosconati, S., Martino, L., Conte, M. R., Mayol, L., Novellino, E., et al. (2011) · Biochimie · doi:10.1016/j.biochi.2011.05.021 · Cited by 24

Molecular characterization of Galectin-8 from Nile tilapia (Oreochromis niloticus Linn.) and its response to bacterial infection

Unajak, S., Pholmanee, N., Songtawee, N., Srikulnath, K., Srisapoome, P., Kiataramkul, A., Kondo, H., Hırono, I., & Areechon, N. (2015) · Molecular Immunology · doi:10.1016/j.molimm.2015.09.012 · Cited by 23

Understanding the Positional Binding and Substrate Interaction of a Highly Thermostable GH10 Xylanase from Thermotoga maritima by Molecular Docking

Yang, J., & Han, Z. (2018) · Biomolecules · doi:10.3390/biom8030064 · Cited by 24

Synthesis and Studies of the Inhibitory Effect of Hydroxylated Phenylpropanoids and Biphenols Derivatives on Tyrosinase and Laccase Enzymes

Dettori, M. A., Fabbri, D., Dessì, A., Dallocchio, R. N., Carta, P., Honisch, C., Ruzza, P., Farina, D., Migheli, R., Serra, P. A., et al. (2020) · Molecules · doi:10.3390/molecules25112709 · Cited by 24

Synthesis, structure elucidation and dft study of a new thiazole–pyridine anchored nnn donor and it's cobalt(II) complex: In-vitro antitumor activity against U937 cancer cells, dna binding property and molecular docking study

Bera, P., Aher, A., Brandão, P., Manna, S. K., Bhattacharyya, I., Pramanik, C., Mandal, B., Das, S., & Bera, P. (2020) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2020.129015 · Cited by 24

Superiority of cilostazol among antiplatelet FDA ‐approved drugs against COVID 19 Mpro and spike protein: Drug repurposing approach

Abosheasha, M. A., & El‐Gowily, A. H. (2020) · Drug Development Research · doi:10.1002/ddr.21743 · Cited by 24

Theoretical Insight into the Library Screening Approach for Binding of Intermolecular G-Quadruplex RNA and Small Molecules through Docking and Molecular Dynamics Simulation Studies

Roy, S., Ali, A., & Bhattacharya, S. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c10991 · Cited by 24

Overexpression of synthesized cephalosporin C acylase containing mutations in the substrate transport tunnel

Wáng, Y., Yu, H., Song, W., An, M., Zhang, J., Luo, H., & Shen, Z. (2011) · Journal of Bioscience and Bioengineering · doi:10.1016/j.jbiosc.2011.08.027 · Cited by 24

Computational characterization of how the VX nerve agent binds human serum paraoxonase 1

Fairchild, S. Z., Peterson, M., Hamza, A., Zhan, C., Cerasoli, D. M., & Chang, W. E. (2010) · Journal of Molecular Modeling · doi:10.1007/s00894-010-0693-9 · Cited by 24

Molecular modeling of human cytochrome P450 2W1 and its interactions with substrates

Li, W., Tang, Y., Hoshino, T., & Neya, S. (2009) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2009.06.002 · Cited by 26

Development and application of site mapping methods for the design of glycosaminoglycans

Agostino, M., Gandhi, N. S., & Mancera, R. L. (2014) · Glycobiology · doi:10.1093/glycob/cwu045 · Cited by 24

Molecular Modeling Study for Inhibition Mechanism of Human Chymase and Its Application in Inhibitor Design

Arooj, M., Kim, S., Sakkiah, S., Cao, G. P., Lee, Y., & Lee, K. W. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062740 · Cited by 24

Flavin Binding to the Deca-heme Cytochrome MtrC: Insights from Computational Molecular Simulation

Breuer, M., Rosso, K. M., & Blumberger, J. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.10.038 · Cited by 24

Targeting of the epidermal growth factor receptor with mesoporphyrin IX-peptide conjugates

Fontenot, K. R., Ongarora, B. G., LeBlanc, L. E., Zhou, Z., Jois, S. D. S., & Vicente, M. G. H. (2016) · Journal of Porphyrins and Phthalocyanines · doi:10.1142/s1088424616500115 · Cited by 24

Kinetic and structural studies on the interactions of Torpedo californica acetylcholinesterase with two donepezil-like rigid analogues

Caliandro, R., Pesaresi, A., Cariati, L., Procopio, A., Oliverio, M., & Lamba, D. (2018) · Journal of Enzyme Inhibition and Medicinal Chemistry · doi:10.1080/14756366.2018.1458030 · Cited by 24

The Current Limits in Virtual Screening and Property Prediction

Hutter, M. C. (2018) · Future Medicinal Chemistry · doi:10.4155/fmc-2017-0303 · Cited by 24

Optical, vibrational (FT-IR and FT-Raman), electronic and molecular docking investigations of 1 Phenyl Isatin

Santhy, K. R., Sweetlin, M. D., Muthu, S., Raja, M., & Abraham, C. S. (2019) · Optik · doi:10.1016/j.ijleo.2019.02.010 · Cited by 24

Dietary flavonoids inhibit the glycation of lens proteins: implications in the management of diabetic cataract

Patil, K. K., Meshram, R. J., Barage, S. H., & Gacche, R. N. (2019) · 3 Biotech · doi:10.1007/s13205-019-1581-3 · Cited by 24

Discovery of Fragment Molecules That Bind the Human Peroxiredoxin 5 Active Site

Barelier, S., Linard, D., Pons, J., Clippe, A., Knoops, B., Lancelin, J., & Krimm, I. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009744 · Cited by 24

Substrate Specificity of Bacterial Prolyl-tRNA Synthetase Editing Domain Is Controlled by a Tunable Hydrophobic Pocket

Kumar, S., Das, M., Hadad, C. M., & Musier‐Forsyth, K. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.313619 · Cited by 24

Classification of Different Approaches for e-Science Applications in Next Generation Computing Infrastructures

Riedel, M., Streit, A., Wolf, F., Lippert, T., & Kranzlmüller, D. A. (2008) · IEEE International Conference on eScience · doi:10.1109/escience.2008.56 · Cited by 24

AI-Enhanced Adaptive Virtual Screening Platform Enabling Exploration of 69 Billion Molecules Discovers Structurally Validated FSP1 InhibitorsPreprint

Cecchini, D., Nigam, A., Tang, M., Reis, J., Koop, M., Gottinger, A., Nicoll, C. R., Wang, Y., Jayaraj, A., Cinaroglu, S. S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.25.537981 · Cited by 24

A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions.

Yang, Z., Liu, Y., Chen, Z., Xu, Z., Shi, J., Chen, K., & Zhu, W. (2015) · Journal of Molecular Modeling · doi:10.1007/s00894-015-2681-6 · Cited by 23

Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors

Giastas, P., Andreou, A., Papakyriakou, A., Koutsioulis, D., Balomenou, S., Tzartos, S. J., Bouriotis, V., & Eliopoulos, E. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b00919 · Cited by 23

Design, synthesis and characterization of new fused pyrazole systems: In Vitro anti-bacterial, anti-fungal, antioxidant evaluation, In Silico DFT and molecular docking studies

Shehab, W. S., Magdy, N., Elhoseni, M. A. R., Assy, M. G., AbdEl-Azim, M. H. M., Mesbah, A. E., El‐Shwiniy, W. H., Amer, M. M., & elsayed, D. A. (2025) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2025.142163 · Cited by 23

Proteomics Analyses of Bacillus subtilis after Treatment with Plumbagin, a Plant-Derived Naphthoquinone

Reddy, P. J., Ray, S., Sathe, G. J., Prasad, T. S. K., Rapole, S., Panda, D., & Srivastava, S. (2015) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2014.0099 · Cited by 23

The Effect of Thiobarbituric Acid on Tyrosinase: Inhibition Kinetics and Computational Simulation

Yin, S., Si, Y.-X., Wang, Z.-J., Wang, S.-F., Oh, S. H., Lee, S., Sim, S.-M., Yang, J.-M., Qian, G.-Y., Lee, J., et al. (2011) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2011.10507398 · Cited by 23

Pentacycloundecane derived hydroxy acid peptides: A new class of irreversible non-scissile ether bridged type isoster as potential HIV-1 wild type C-SA protease inhibitors

Karpoormath, R. V., Sayed, Y., Govender, P., Govender, T., Kruger, H. G., Soliman, M. E. S., & Maguire, G. E. M. (2011) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2011.08.002 · Cited by 23

Rational Prediction with Molecular Dynamics for Hit Identification

Nichols, S. E., Swift, R. V., & Amaro, R. E. (2012) · Current Topics in Medicinal Chemistry · doi:10.2174/156802612804910313 · Cited by 22

An in vivo and in silico approach to elucidate the tocotrienol-mediated fortification against infection and inflammation induced alterations in antioxidant defense system.

Khan, M. S., Khan, M. K. A., Siddiqui, M. H., & Arif, J. M. (2011) · PubMed · Cited by 23

Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms

Sulimov, A. V., Zheltkov, D. A., Oferkin, I. V., Kutov, D. C., Katkova, E. V., Tyrtyshnikov, E. E., & Sulimov, V. B. (2017) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2017.02.004 · Cited by 23

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

Huey, R., Morris, G. M., Olson, A. J., & Goodsell, D. S. (2007) · Cited by 45

Software News and Update A Semiempirical Free Energy Force Field

Desolvation, C.-B., Huey, R., Morris, G. M., Olson, A. J., & Goodsell, D. S. (2014)

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

Raschka, S. (2014) · doi:10.13140/2.1.5097.1528 · Cited by 4

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

Forli, S., & Olson, A. J. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm2005145 · Cited by 290