This paper is in the following e-collection/theme issue:

Tutorial (1)

Published on in Vol 1, No 1 (2020): Inaugural Issue

Preprints (earlier versions) of this paper are available at https://preprints.jmir.org/preprint/14232, first published .
Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians

Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians

Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians

Authors of this article:

Sania Safdar Butt1 Author Orcid Image ;   Yasmin Badshah1 Author Orcid Image ;   Maria Shabbir1 Author Orcid Image ;   Mehak Rafiq2 Author Orcid Image
Article Authors Cited by (75) Tweetations (3) Metrics

Journals

  1. Kundu D, Dubey V. Potential alternatives to current cholinesterase inhibitors: anin silicodrug repurposing approach. Drug Development and Industrial Pharmacy 2021;47(6):919 View
  2. Raman A, Kumari K, Jain P, Vishvakarma V, Kumar A, Kaushik N, Choi E, Kaushik N, Singh P. In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19. Pharmaceutics 2022;14(1):135 View
  3. Ha W, Yamaguchi T, Iwakami S, Sunohara Y, Matsumoto H. Comparison of herbicide specificity of CYP81A cytochrome P450s from rice and a multiple‐herbicide resistant weed, Echinochloa phyllopogon. Pest Management Science 2022;78(10):4207 View
  4. Bodourian C, Poudel N, Papageorgiou A, Antoniadi M, Georgakis N, Abe H, Labrou N. Ligandability Assessment of Human Glutathione Transferase M1-1 Using Pesticides as Chemical Probes. International Journal of Molecular Sciences 2022;23(7):3606 View
  5. Azemin W, Alias N, Ali A, Shamsir M. In silico analysis prediction of HepTH1-5 as a potential therapeutic agent by targeting tumour suppressor protein networks. Journal of Biomolecular Structure and Dynamics 2023;41(4):1141 View
  6. Haitham Ahmed A, Zaher Samman T. In silico disrupting quorum sensing of porphyromonas gingivalis via essential oils and coumarin derivatives. Annals of Proteomics and Bioinformatics 2022;6(1):001 View
  7. Kurze E, Ruß V, Syam N, Effenberger I, Jonczyk R, Liao J, Song C, Hoffmann T, Schwab W. Glucosylation of (±)-Menthol by Uridine-Diphosphate-Sugar Dependent Glucosyltransferases from Plants. Molecules 2021;26(18):5511 View
  8. Chandrasekaran R, Murugavel S, Guin M, Silambarasan T. Crystal structure, Hirshfeld, computational biomolecular investigations, and MTT assay studies of amino pyrimidine derivative as EGFR kinase domain inhibitor. Journal of Molecular Structure 2022;1254:132416 View
  9. Alkandahri M, Patala R, Berbudi A, Subarnas A. Antimalarial activity of curcumin and kaempferol using structure-based drug design method. Journal Of Advanced Pharmacy Education And Research 2021;11(4):86 View
  10. Azemin W, Alias N, Ali A, Shamsir M. Structural and functional characterisation of HepTH1-5 peptide as a potential hepcidin replacement. Journal of Biomolecular Structure and Dynamics 2023;41(2):681 View
  11. Anwar W, Abdel-maksoud F, Sayed A, Abdel-Rahman I, Makboul M, Zaher A. Potent hepatoprotective activity of common rattan (Calamus rotang L.) leaf extract and its molecular mechanism. BMC Complementary Medicine and Therapies 2023;23(1) View
  12. Chiu P, Huang W, Hsu H, Huang W, Wu Y, Rachel Cheng T, Fang J. Designing a bis-azide photoaffinity probe in labeling influenza nucleoprotein trimer to give an insight into the binding mode. European Journal of Medicinal Chemistry Reports 2022;6:100091 View
  13. Nabil-Adam A, Ashour M, Shreadah M. The hepatoprotective candidates by synergistic formula of marine and terrestrial against Acetaminophen toxicity using in-vitro, in-vivo, and in silico screening approach. Saudi Journal of Biological Sciences 2023;30(4):103607 View
  14. Jawale P, Bhanage B. Kinetic and docking study of synthesis of glyceryl monostearate by immobilized lipase in non-aqueous media. Biocatalysis and Biotransformation 2023;41(2):123 View
  15. Varghese N, Jose J, Krishna P, Philip D, Joy F, Vinod T, Prathapachandra Kurup M, Nair Y. In vitro Analytical Techniques as Screening Tools to investigate the Metal chelate‐DNA interactions. ChemistrySelect 2023;8(5) View
  16. Bhimanwar R, Lokhande K, Shrivastava A, Singh A, Chitlange S, Mittal A. Identification of potential drug candidates as TGR5 agonist to combat type II diabetes using in silico docking and molecular dynamics simulation studies. Journal of Biomolecular Structure and Dynamics 2023;41(22):13314 View
  17. Cauilan A, Ruiz C. Sodium Malonate Inhibits the AcrAB-TolC Multidrug Efflux Pump of Escherichia coli and Increases Antibiotic Efficacy. Pathogens 2022;11(12):1409 View
  18. Moloudizargari M, Hekmatirad S, Gharaghani S, Moghadamnia A, Najafzadehvarzi H, Asghari M. Virtual screening reveals aprepitant to be a potent inhibitor of neutral sphingomyelinase 2: implications in blockade of exosome release in cancer therapy. Journal of Cancer Research and Clinical Oncology 2023;149(10):7207 View
  19. Dobryakova N, Zhdanov D, Sokolov N, Aleksandrova S, Pokrovskaya M, Kudryashova E. Rhodospirillum rubrum L-Asparaginase Conjugates with Polyamines of Improved Biocatalytic Properties as a New Promising Drug for the Treatment of Leukemia. Applied Sciences 2023;13(5):3373 View
  20. Çağlar Yavuz S. Molecular docking studies and structural&electronic analysis of gefarnate. Journal of the Indian Chemical Society 2023;100(4):100971 View
  21. Pande M, Kundu D, Srivastava R. Selective vitamins as potential options for dietary therapeutic interventions: In silico and In vitro insights from mutant C terminal fragment of FGA. The Journal of Steroid Biochemistry and Molecular Biology 2023;230:106290 View
  22. Chagas R, Otsuka F, Pineda M, Salinas R, Marana S. Mechanism of imidazole inhibition of a GH1 β‐glucosidase. FEBS Open Bio 2023;13(5):912 View
  23. Mir S, Madkhali Y, Firoz A, Al Othaim A, Alturaiki W, Almalki S, Algarni A, Alsagaby S. Inhibitory Potential of the Ocimum sanctum Phytochemicals on Bruton’s Tyrosine Kinase, a Well-Known Drug Target for Treatment of Chronic Lymphocytic Leukemia: An In Silico Investigation. Molecules 2023;28(8):3287 View
  24. Mohan L, Lee J, Srinivasarao M, Cutright A, Raju S, Stokes S, Emerson J, Kim J. Cu‐Catalyzed Cross‐Coupling Reactions of Enamines and Terminal Alkynes: Access of Propargylamines as Neurodegenerative Disorder Agents. Asian Journal of Organic Chemistry 2023;12(10) View
  25. Khatana K, Gupta A, Ghosal A, Dey P, Zafar F, Srivastava A, Verma P. In silico identification and validation of phenolic lipids as potential inhibitor against bacterial and viral strains. Journal of Biomolecular Structure and Dynamics 2024;42(5):2525 View
  26. Padilla-Vaca F, de la Mora J, García-Contreras R, Ramírez-Prado J, Vicente-Gómez M, Vargas-Gasca F, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Cuéllar-Mata P, Vargas-Maya N, Franco B. Theoretical study of ArcB and its dimerization, interaction with anaerobic metabolites, and activation of ArcA. PeerJ 2023;11:e16309 View
  27. Wasilewski T, Neubauer D, Wojciechowski M, Szulczyński B, Gębicki J, Kamysz W. Evaluation of Linkers’ Influence on Peptide-Based Piezoelectric Biosensors’ Sensitivity to Aldehydes in the Gas Phase. International Journal of Molecular Sciences 2023;24(13):10610 View
  28. Kusuma Djati F, Agustina D, Mustofa , Nirwati H, Widada J, Damayanti E, Susilowati H, Kristina S, Hsu M, Syahrom A, Ismail H, Vo T. In Silico Destruction of Porphyromonas gingivalis Fimbriae by Streptomyces sp. Strain GMY02. BIO Web of Conferences 2023;75:02004 View
  29. ÇAĞLAR YAVUZ S. Molecular Docking and Reactive Sites Identification (Homo–Lumo, Mep) of Allicin and Diallyl Disulfide: Potential Anticancer Inhibitor. Karadeniz Fen Bilimleri Dergisi 2023;13(4):1523 View
  30. Rajimon K, Nair D, Srinivasaragavan D, Thomas R. Integrated experimental and computational study of a fluorescent Schiff base: Synthesis, characterization, electronic structure properties, and biological potentials of (1E,1’E)-1,1’-(1,4-phenylene) bis(N-(2-chlorophenyl) methanimine) with a focus on molecular docking and dynamics simulation. Chemical Physics Impact 2024;8:100435 View
  31. Orozco M, Moreno P, Guevara M, Abonia R, Quiroga J, Insuasty B, Barreto M, Burbano M, Crespo-Ortiz M. In silico prediction and in vitro assessment of novel heterocyclics with antimalarial activity. Parasitology Research 2024;123(1) View
  32. Singh S, Kancharla S, Kolli P, Mandadapu G, Jena M. In Silico Exploration of Phytochemicals as Potential Drug Candidates against Dipeptidyl Peptidase-4 Target for the Treatment of Type 2 Diabetes. Biomedical and Biotechnology Research Journal (BBRJ) 2023;7(4):598 View
  33. Alsakhen N, Radwan E, Zafer I, Abed alfattah H, Shamkh I, Rehman M, Shahwan M, Khan K, Ahmed S. Computational analysis of bevacizumab binding with protein receptors for its potential anticancer activity. Journal of Biomolecular Structure and Dynamics 2024:1 View
  34. Kurosawa M, Kato F, Hishiki T, Ito S, Fujisawa H, Yamaguchi T, Moriguchi M, Hosokawa K, Watanabe T, Saito-Tarashima N, Minakawa N, Fujimuro M. Sofosbuvir Suppresses the Genome Replication of DENV1 in Human Hepatic Huh7 Cells. International Journal of Molecular Sciences 2024;25(4):2022 View
  35. Biswas S, Roy J. Phytocompounds as potential inhibitors of mycobacterial multidrug efflux pump Rv1258c: an in silico approach. AMB Express 2024;14(1) View
  36. Alawam A, M. Alneghery L, Alwethaynani M, Alamri M. A hierarchical approach towards identification of novel inhibitors against L, D-transpeptidase YcbB as an anti-bacterial therapeutic target. Journal of Biomolecular Structure and Dynamics 2024:1 View
  37. Enggi C, Sulistiawati S, Himawan A, Raihan M, Iskandar I, Saputra R, Rahman L, Yulianty R, Manggau M, Donelly R, Aswad M, Permana A. Application of Biomaterials in the Development of Hydrogel-Forming Microneedles Integrated with a Cyclodextrin Drug Reservoir for Improved Pharmacokinetic Profiles of Telmisartan. ACS Biomaterials Science & Engineering 2024;10(3):1554 View
  38. Sulistiawati S, Kristina Enggi C, Wiyulanda Iskandar I, Rachmad Saputra R, Sartini S, Rifai Y, Rahman L, Aswad M, Dian Permana A. Bioavailability enhancement of sildenafil citrate via hydrogel-forming microneedle strategy in combination with cyclodextrin complexation. International Journal of Pharmaceutics 2024;655:124053 View
  39. Taxak B, Devi J, Kumar B, Arora T. Hydrazone-containing organotin(IV) complexes: synthesis, characterization, antimicrobial, antioxidant activity and molecular-docking studies. BioMetals 2024;37(5):1079 View
  40. AKKAYA H, SÜMER E. IN SILICO APPROACHES ON PHENYLALANINE HYDROXYLASE INHIBITOR-RELATED COMPOUNDS USED IN PARKINSON’S DISEASE TREATMENT. Ankara Universitesi Eczacilik Fakultesi Dergisi 2024;48(2):11 View
  41. Ramírez‐Prada J, Rocha‐Ortiz J, Orozco M, Moreno P, Guevara M, Barreto M, Burbano M, Robledo S, Crespo‐Ortiz M, Quiroga J, Abonia R, Cuartas V, Insuasty B. New pyridine‐based chalcones and pyrazolines with anticancer, antibacterial, and antiplasmodial activities. Archiv der Pharmazie 2024;357(7) View
  42. Fukawa E, Suzuki Y, Adachi T, Miyata T, Makino F, Tanaka H, Namba K, Sowa K, Kitazumi Y, Shirai O. Structural and electrochemical elucidation of biocatalytic mechanisms in direct electron transfer-type D-fructose dehydrogenase. Electrochimica Acta 2024;490:144271 View
  43. Promtang S, Sanguanphun T, Chalorak P, Pe L, Niamnont N, Sobhon P, Meemon K. 2-Butoxytetrahydrofuran, Isolated from Holothuria scabra, Attenuates Aggregative and Oxidative Properties of α-Synuclein and Alleviates Its Toxicity in a Transgenic Caenorhabditis elegans Model of Parkinson’s Disease. ACS Chemical Neuroscience 2024;15(11):2182 View
  44. Do H, Pirayesh E, Ferreira G, Pandhare A, Gallardo Z, Jansen M. A bupropion modulatory site in the Gloeobacter violaceus ligand-gated ion channel. Biophysical Journal 2024;123(14):2185 View
  45. Nawaz M, Khalid H, Shahbaz S, Al-Ghanim K, Pugazhendhi A, Zhu D. Discovery of putative inhibitors of human Pkd1 enzyme: Molecular docking, dynamics and simulation, QSAR, and MM/GBSA. Environmental Research 2024;257:119336 View
  46. Ali M, Hassan M, Ansari S, Alkahtani H, Al-Rasheed L, Ansari S. Quercetin and Kaempferol as Multi-Targeting Antidiabetic Agents against Mouse Model of Chemically Induced Type 2 Diabetes. Pharmaceuticals 2024;17(6):757 View
  47. Kumar V, Bhukal A, Raman A, Singh P, Lal K. Synthesis, Characterization, Antimicrobial and In Silico Studies of Isatin Schiff Base Linked 1,2,3‐Triazole Hybrids. Chemistry & Biodiversity 2024;21(7) View
  48. Çağlar Yavuz S. Quantum Chemical Computations, Molecular Docking, and ADMET Predictions of Cynarin. Bitlis Eren Üniversitesi Fen Bilimleri Dergisi 2024;13(2):460 View
  49. Yu Z, Khan M, Atta M, Lodhi M, Muhammad S. Unveiling the potential of Traditional Chinese Medicines in combating NorA-mediated S. aureus drug resistance. A molecular dynamic study. Inorganic Chemistry Communications 2024;167:112771 View
  50. Abd Ghani M, Abu Bakar N, Ramadani A, Nugraha A, Awang K, Che Omar M, Supratman U, Kamarulzaman E, Mohamad Taib M. Hemisynthesis of Pentacyclic Triterpenoids from Diospyros foxworthyi with In vitro and In silico Anti-malarial Evaluation. Current Organic Chemistry 2024;28(10):799 View
  51. Li Z, Miao L, Ren G, Wang H, Shangguan L, Zhao H, Li X. Weighted gene coexpression network analysis and machine learning for the determination of tfh cell and B cell infiltrating biomarkers in thymoma-associated myasthenia gravis. Heliyon 2024;10(14):e34364 View
  52. Ananya , Panchariya D, Karthic A, Singh S, Mani A, Chawade A, Kushwaha S. Vaccine design and development: Exploring the interface with computational biology and AI. International Reviews of Immunology 2024;43(6):361 View
  53. Akkaya H, Özmaldar A. IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS. Ankara Universitesi Eczacilik Fakultesi Dergisi 2024;48(3):19 View
  54. Putri R, Enggi C, Sulistiawati S, Burhanuddin H, Iskandar I, Saputra R, Rahman L, Sartini S, Rifai Y, Aswad M, Permana A. Development of itraconazole ocular delivery system using β-cyclodextrin complexation incorporated into dissolving microneedles for potential improvement treatment of fungal keratitis. Journal of Biomaterials Science, Polymer Edition 2024;35(15):2315 View
  55. Yavuz S. Synthesis of new two 1,2-disubstituted benzimidazole compounds: their in vitro anticancer and in silico molecular docking studies. BMC Chemistry 2024;18(1) View
  56. Chen J, Ni D, Zhu Y, Xu W, Moussa T, Zhang W, Mu W. Discovery of a Thermostable Tagatose 4-Epimerase Powered by Structure- and Sequence-Based Protein Clustering. Journal of Agricultural and Food Chemistry 2024;72(33):18585 View
  57. Wang L. People management, diversity practices and workforce productivity: Basis for development of strategic IT optimization. International Journal of Research Studies in Management 2024;12(10) View
  58. Saadan N, Ahmed W, Kadi A, Al-Mutairi M, Al-Wabli R, Rahman A. Synthesis and Evaluation of Thiazolyl-indole-2-carboxamide Derivatives as Potent Multitarget Anticancer Agents. ACS Omega 2024;9(40):41944 View
  59. Mande S, Repudi L, Goswami S, Nallasivan P, Gandla K. Exploring compound suitability and employing DFT calculations, molecular docking, and dynamics simulation to investigate potent compounds from podophyllum medicinal plants for breast cancer therapy. Bulletin of the National Research Centre 2024;48(1) View
  60. Bernardo A, Mohammed-Sadhakathullah A, Angelucci C, Estrany F, Berghella A, Torras J, Armelin E, Oddi S, Dainese E. Non-enzymatic cholesterol biosensor: Electrochemical sensing based on peptide-polylactic acid thin film. International Journal of Biological Macromolecules 2024;281:136337 View
  61. Baba A, Shah A, Bayil I, Nayak S, Shyanti R, Nissa N, Muzaffar M, Hajam M, Akhtar R, Malla B, Akhtar S, Singh R, Dar N. Polydatin inhibits histone deacetylase 1 and shows an anti-angiogenic action in head and neck squamous cell carcinoma. Medical Oncology 2024;41(11) View
  62. Kaur H, Swadia D, Sinha S. Bile Acids as Modulators of α-Synuclein Aggregation: Implications for Parkinson’s Therapy. ACS Chemical Neuroscience 2024;15(21):4055 View
  63. Tung D, Dung D, Cong N, Hai D, Baecker D, Ngo S, Dung P, Thuan N, Nam N, An N. Harmonizing QSAR Machine Learning‐Based Models and Docking Approaches for Identifying Novel Histone Deacetylase 2 Inhibitors. ChemistrySelect 2024;9(40) View
  64. Zeb M, Dumont E, Khan M, Shehzadi A, Ahmad I. Multi-Epitopic Peptide Vaccine Against Newcastle Disease Virus: Molecular Dynamics Simulation and Experimental Validation. Vaccines 2024;12(11):1250 View
  65. Badr M, Elmongy E, Elkhateeb D, Moemen Y, Khalil A, Ali H, Binsuwaidan R, Awadallah F, El Sayed I. In Silico and In Vitro Investigation of Cytotoxicity and Apoptosis of Acridine/Sulfonamide Hybrids Targeting Topoisomerases I and II. Pharmaceuticals 2024;17(11):1487 View
  66. Salaam R, Tarkaa C, Ebuh R, Olaniyi D, Oladokun S, Sowemimo R, Ajayi O, Akangbe O. In silico discovery of potential androgen receptor and cytochrome P450 17A1 inhibitors from Camellia sinensis for prostate cancer treatment. Next Research 2024;1(2):100068 View
  67. Sun P, Niu L, He P, Yu H, Chen J, Cui H, Li X. Trp-574-Leu and the novel Pro-197-His/Leu mutations contribute to penoxsulam resistance in Echinochloa crus-galli (L.) P. Beauv.. Frontiers in Plant Science 2024;15 View
  68. Shikha R, Kar S. Evaluation of molecular inclusion of azole antifungals by β-cyclodextrin using computational molecular approach. Discover Chemistry 2024;1(1) View
  69. Loganathan V, Mani A, Ahamed A, Idhayadhulla A, Biresaw G, Manilal A. Synthesis of 4-Hydroxy Coumarin Hybrid with 2H-Thiopyran and Imidazolidine-2,4-Dione Derivatives and the Investigation of their Antimicrobial, Anticoagulant and Cytotoxic Activities, and Molecular Docking. Chemistry Africa 2024;7(10):5257 View
  70. Kuila A, Maity R, Acharya P, Sarkar T, Bhakat A, Brandao P, Pattanayak S, Maity T, Dalai S, Sarkar K, Samanta B. Exploring the Potential Fungicidal Applications of a Cu(II) Complex with Schiff Base and Carboxylates against Fusarium equisetum. ACS Omega 2024;9(49):48273 View
  71. Mohammadnezhad P, Valdés A, Cifuentes A. Optimization and Chemical Characterization of Extracts Obtained from Ferula persica var. latisecta Aerial Parts and Roots and Their Neuroprotective Evaluation. Nutrients 2024;16(23):4210 View
  72. Nabi T, Riyed T, Ornob A, Umar S. Deep learning based predictive modeling to screen natural compounds against TNF-alpha for the potential management of rheumatoid arthritis: Virtual screening to comprehensive in silico investigation. PLOS ONE 2024;19(12):e0303954 View
  73. Bozkurt İ, Sabancilar İ, Kiliç Ö, Bayrakdar A, Paçal N, Aras A. The Effects of Lamium garganicum L. Subsp. lasioclades (Stapf.) R. Mill Plant Against Fibroblast (U2OS Cell), Acetylcholinesterase, Glutathione S‐Transferase: An In Vitro, In Silico Biological Activity Screening Study. Chemistry & Biodiversity 2024 View

Books/Policy Documents

  1. Kesh M, Ghosh A, Biswas D. Computational Methods for Rational Drug Design. View