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

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 2023:1 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 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 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 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: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 2024:1 View