AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4

Abstract AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force field for metalloproteins. AMDock integrates several external programs (Open Babel, PDB2PQR, AutoLigand, ADT scripts) to accurately prepare the input structure files and to optimally define the search space, offering several alternatives and different degrees of user supervision. For visualization of molecular structures, AMDock uses PyMOL, starting it automatically with several predefined visualization schemes to aid in setting up the box defining the search space and to visualize and analyze the docking results. One particularly useful feature implemented in AMDock is the off-target docking procedure that allows to conduct ligand selectivity studies easily. In summary, AMDock’s functional versatility makes it a very useful tool to conduct different docking studies, especially for beginners. The program is available, either for Windows or Linux, at https://github.com/Valdes-Tresanco-MS. Reviewers This article was reviewed by Alexander Krah and Thomas Gaillard.

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DESIGN AND MOLECULAR DOCKING STUDIES OF NOVEL ANTIMICROBIAL PEPTIDES USING AUTODOCK MOLECULAR DOCKING SOFTWARE

Asian Journal of Pharmaceutical and Clinical Research ◽

10.22159/ajpcr.2017.v10s4.21332 ◽

2017 ◽

Vol 10 (16) ◽

pp. 28 ◽

Cited By ~ 1

Author(s):

Kiranpreet Kaur ◽

Paranjeet Kaur ◽

Amit Mittal ◽

Surendra Kumar Nayak ◽

Gopal L Khatik

Keyword(s):

Amino Acids ◽

Molecular Docking ◽

Antimicrobial Peptides ◽

Binding Affinity ◽

Docking Studies ◽

Molecular Structures ◽

Short Chain ◽

Receptor Protein ◽

Autodock Vina ◽

E Coli

Objective: Design of novel antimicrobial peptides and study through the molecular docking.Methods: The molecular structures were drawn in ChemBiodraw ultra and by the help of ChemBiodraw 3D, all structures were energy minimized by theMM2 method and converted to pdbextension file which is readable at the ADT interface. The AutoDock Vina (ADT) 1.5.6 software is used for molecular docking purposes.Results: Eight antimicrobial peptides (AMPs) were designed based on theMP196antimicrobial peptide. Among these KP_03R (FWRWRW-NH2) showed good binding affinity. These peptides also showed the stereochemical influence on affinity toward the3vma protein of E. coli, where AMP with R stereochemistry showed better activity than its opposite stereochemistry. Conclusion: Novel AMPs were designed by modifications on the MP196 a short chain of amino acids antimicrobial peptides. Molecular docking software was used to determine the binding affinity between drug and receptor protein. Among all the designed peptides KP_03R(FWRWRW-NH2) showed the maximum binding affinity against thepenicillin-binding protein of E.coli and also exhibited stereoselective activity.

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MOLECULAR DOCKING AND PHARMACOKINETIC PREDICTION OF HERBAL DERIVATIVES AS MALTASE-GLUCOAMYLASE INHIBITOR

Asian Journal of Pharmaceutical and Clinical Research ◽

10.22159/ajpcr.2017.v10i9.19337 ◽

2017 ◽

Vol 10 (9) ◽

pp. 392 ◽

Cited By ~ 1

Author(s):

Peter Juma Ochieng ◽

Tony Sumaryada ◽

Daniel Okun

Keyword(s):

Molecular Docking ◽

Surface Area ◽

Docking Studies ◽

Polar Surface Area ◽

Autodock Vina ◽

Standard Drug ◽

Lipinski’S Rule ◽

Structure Activity ◽

Topological Polar Surface Area ◽

High Binding Affinity

Objective: To perform molecular docking and pharmacokinetic prediction of momordicoside F2, beta-sitosterol, and cis-N-feruloyltyramine herbal derivatives as maltase-glucoamylase (MGAM) inhibitors for the treatment of diabetes.Methods: The herbal derivatives and standard drug miglitol were docked differently onto MGAM receptor using AutoDock Vina software. In addition, Lipinski’s rule, drug-likeness, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties were analyzed using Molinspiration, ADMET structure–activity relationship, and prediction of activity spectra for substances online tools.Results: Docking studies reveal that momordicoside F2, beta-sitosterol, and cis-N-feruloyltyramine derivatives have high binding affinity to the MGAM receptor (−7.8, −6.8, and −6.5 Kcal/Mol, respectively) as compared to standard drug miglitol (−5.3 Kcal/Mol). In addition, all the herbal derivatives indicate good bioavailability (topological polar surface area <140 Ȧ and Nrot <10) without toxicity or mutagenic effects.Conclusion: The molecular docking and pharmacokinetic information of herbal derivatives obtained in this study can be utilized to develop novel MGAM inhibitors having antidiabetic potential with better pharmacokinetic and pharmacodynamics profile.

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Synthesis and Molecular Docking Studies of Coumarinyl Thiazole as Cell Division Protein Kinase 2 Inhibitor

Asian Journal of Chemistry ◽

10.14233/ajchem.2019.22106 ◽

2019 ◽

Vol 31 (11) ◽

pp. 2453-2456

Author(s):

J. Brindha ◽

T.F. Abbs Fen Reji

Keyword(s):

Molecular Docking ◽

Cell Division ◽

Protein Kinase ◽

Screening Tool ◽

Docking Study ◽

Docking Studies ◽

Autodock Vina ◽

Molecular Docking Study ◽

Molecular Docking Studies ◽

Cell Division Protein

A series of 2-alkylamino-4-(3-coumarinyl)thiazoles were synthesized, characterized and evaluated their anticancer activity through molecular docking studies. Cell division protein kinase 2 (PDB code: 1KE9) is selected as a target and the compounds which obeys Lipinski rule of five is selected as a ligand. Molecular docking study is carried out using AutoDock Vina in PyRx virtual screening tool. This study revealed that all the compounds are active against the molecular target and compounds 5a and 5c have the highest docking score.

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IDENTIFICATION OF NOVEL 5-STYRYL-1,2,4-OXADIAZOLE/TRIAZOLE DERIVATIVES AS THE POTENTIAL ANTI-ANDROGENS THROUGH MOLECULAR DOCKING STUDY

International Journal of Pharmacy and Pharmaceutical Sciences ◽

10.22159/ijpps.2016v8i10.13844 ◽

2016 ◽

Vol 8 (10) ◽

pp. 72 ◽

Cited By ~ 3

Author(s):

Paranjeet Kaur ◽

Gopal L. Khatik

Keyword(s):

Molecular Docking ◽

Androgen Receptor ◽

Binding Affinity ◽

Docking Study ◽

Molecular Structures ◽

The Novel ◽

Autodock Vina ◽

Molecular Docking Study ◽

Triazole Derivatives ◽

Better Than

Objective: To identify the novel and simple bioactive antiandrogens, that can overcome to side effects as well as drug resistance.Methods: The AutoDock Vina (ADT) 1.5.6 software is used for molecular docking purposes. The molecular structures were drawn in ChemBiodraw ultra and by the help of ChemBiodraw 3D, all structures were energy minimized by MM2 method and converted to pdb extension file which is readable at the ADT interface.Results: Total ten compounds from both series were shown better binding affinity than R-bicalutamide including oxadiazole and triazole series. Among these pk42 and pk46 were studied in-depth which showed best binding affinity to the androgen receptor. The cis-isomers were found better than their trans-isomer.Conclusion: Novel 5-styryl-1,2,4-oxadiazole/triazole derivatives were studied through molecular modeling using Autodock Vina. The potent compounds which showed better binding affinity than R-bicalutamide like pk24 and 46 were further analyzed for their interactions. The conformational effect also found significant in binding to the androgen receptor.

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Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians

JMIR Bioinformatics and Biotechnology ◽

10.2196/14232 ◽

2020 ◽

Vol 1 (1) ◽

pp. e14232

Author(s):

Sania Safdar Butt ◽

Yasmin Badshah ◽

Maria Shabbir ◽

Mehak Rafiq

Keyword(s):

Molecular Docking ◽

San Francisco ◽

Target Protein ◽

Autodock Vina ◽

Protein Database ◽

Computational Docking ◽

Chemical Systems ◽

Modern Drug ◽

User Friendly ◽

Ucsf Chimera

In the field of drug discovery, many methods of molecular modeling have been employed to study complex biological and chemical systems. Experimental strategies are integrated with computational approaches for the identification, characterization, and development of novel drugs and compounds. In modern drug designing, molecular docking is an approach that explores the confirmation of a ligand within the binding site of a macromolecule. To date, many software and tools for docking have been employed. AutoDock Vina (in UCSF [University of California, San Francisco] Chimera) is one of the computationally fastest and most accurate software employed in docking. In this paper, a sequential demonstration of molecular docking of the ligand fisetin with the target protein Akt has been provided, using AutoDock Vina in UCSF Chimera 1.12. The first step involves target protein ID retrieval from the protein database, the second step involves visualization of the protein structure in UCSF Chimera, the third step involves preparation of the target protein for docking, the fourth step involves preparation of the ligand for docking, the fifth step involves docking of the ligand and the target protein as Mol.2 files in Chimera by using AutoDock Vina, and the final step involves interpretation and analysis of the docking results. By following the guidelines and steps outlined in this paper, researchers with no previous background in bioinformatics research can perform computational docking in an easier and more user-friendly manner.

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Ligand docking and binding site analysis with pymol and autodock/vina

International Journal of Basic and Applied Sciences ◽

10.14419/ijbas.v4i2.4123 ◽

2015 ◽

Vol 4 (2) ◽

pp. 168 ◽

Cited By ~ 7

Author(s):

Mohd. Ahmar Rauf ◽

Swaleha Zubair ◽

Asim Azhar

Keyword(s):

Molecular Docking ◽

Drug Design ◽

Three Dimensional ◽

Structural Features ◽

Docking Studies ◽

Ligand Docking ◽

Structure Based Drug Design ◽

Site Analysis ◽

User Friendly ◽

Autodock 4.2

Docking of various therapeutically important chemical entities to the specific target sites offers a meaningful strategy that may have tremendous scope in a drug design process. For a thorough understanding of the structural features that determine the strength of bonding between a ligand with its receptor, an insight to visualize binding geometries and interaction is mandatory. Bioinformatical as well as graphical software ‘PyMOL’ in combination with the molecular docking suites Autodock and Vina allows the study of molecular combination to visualize and understand the structure-based drug design efforts. In the present study, we outlined a user friendly method to perform molecular docking using vina and finally the results were analyzed in pymol in both two as well as three-dimensional orientation. The operation bypasses the steps that are involved in docking using cygwin terminal like formation of gpf and dpf files. The simple and straight-forward operation method does not require formal bioinformatics training to apprehend molecular docking studies using AutoDock 4.2 program.

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SAR and Pharmacophore Based Designing of Some Antimalarial and Antiretroviral Agents: An INTERNET Based Drug Design Approach

American Journal of Undergraduate Research ◽

10.33697/ajur.2013.007 ◽

2013 ◽

Vol 11 (3 and 4) ◽

Author(s):

Soumendranath Bhakat

Keyword(s):

Molecular Docking ◽

Drug Discovery ◽

Drug Design ◽

Computational Chemistry ◽

Operating Systems ◽

Docking Studies ◽

Computational Tools ◽

Structure Activity ◽

System Configurations ◽

User Friendly

With the development of computational chemistry and molecular docking studies, Structure Activity Relationship or SAR- and pharmacophore-based drug design have been modified to target based drug discovery using sophisticated computational tools which is not very much user friendly and has got many incompatibility issues with many operating systems (OS) and other system configurations. In this paper SAR and pharmacophore based drug design approaches have been described by the used of free internet based tools which are very much user friendly and can almost compatible with any platform. Some antimalarial. And anti retroviral agents have been designed using pharmacophore study and their drug like properties, toxicity, metabolic sites and other parameters are predicted by the free internet based tools.

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In silico molecular docking studies of some phytochemicals against peroxisome-proliferator activated receptor gamma (PPAR-γ)

GSC Biological and Pharmaceutical Sciences ◽

10.30574/gscbps.2018.5.2.0085 ◽

2018 ◽

Vol 5 (2) ◽

pp. 001-005

Author(s):

H. A. Ahmed ◽

I. Y. Alkali

Keyword(s):

Molecular Docking ◽

Insulin Sensitivity ◽

Binding Affinity ◽

Docking Studies ◽

Peroxisome Proliferator ◽

Autodock Vina ◽

Peroxisome Proliferator Activated Receptor ◽

Standard Drug ◽

Molecular Docking Studies ◽

Ppar Γ

Peroxisome Proliferator-Activated Receptor-γ (PPAR-γ) is a ligand-activated transcription factor and a member of the nuclear receptor superfamily that regulate the gene expression of proteins involved in glucose, lipid metabolism, adipocyte proliferation and differentiation and insulin sensitivity. Thiazolidinediones (TZDs) are one important class of synthetic agonists of PPAR-γ. TZDs are antidiabetic agents that target adipose tissue and improve insulin sensitivity, and they are currently being used in the treatment of type 2 diabetes. The study was carried out in order to discover new phytochemicals that have the ability to stimulate the PPAR-γ using molecular docking studies. AutoDock vina was used as molecular-docking tool in order to carry out the docking simulations. Nine phytochemicals namely plumbagin, quercetin, isovitexin, mangiferin, syringin, lupe-20-ene-3-one, purine 2, 6-dione, diosmetin and β sitosterol and pioglitazone a standard drug were docked against PPAR-γ using AutoDock vina and the results were analyzed using binding affinity. The results revealed that the compounds have significant binding affinity towards the PPAR-γ comparable to pioglitazone the standard drug. Based on the findings of this study these phytochemicals can serve as source of antidiabetic drugs via the mechanism of inhibition of PPAR-γ.

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Molecular Docking Studies on Phenolic Constituents of Anethum graveolens L. Seed Extracts

Journal of Pharmaceutical Research International ◽

10.9734/jpri/2021/v33i56b33939 ◽

2021 ◽

pp. 119-128

Author(s):

Paul Andrei Negru ◽

Sanda Rodica Bota ◽

Oana Delia Stanasel ◽

Cristian Felix Blidar ◽

Georgeta Serban

Keyword(s):

Antioxidant Activity ◽

Molecular Docking ◽

Docking Studies ◽

Autodock Vina ◽

Anethum Graveolens ◽

Inhibitory Potency ◽

Molecular Docking Studies ◽

Discovery Studio ◽

Phenolic Constituents ◽

Seed Extracts

Background: There are studies indicating that aqueous or hydroalcoholic dill extracts showed higher antioxidant activity compared to other fractions. Molecular docking studies would be relevant to get information on the mechanism of action of the phenolic constituents of Anethum graveolens seed extracts as bioactive compounds. Methodology: In order to perform the docking studies of antioxidant activity of phenolic constituents of Anethum graveolens seed extracts, BIOVIA Discovery Studio and AutoDock Vina software were used. Results: The orientation of flavonoids within Hck and CYP2C9 binding sites has been shown to be the main reason for their inhibitory potency. Conclusion: Molecular docking studies indicate that the compounds identified interact with the target enzymes Hck and CYP2C9 at molecular level through their condensed ring systems and hydroxyl substituents and therefore support the antioxidant capacity of the studied phenolic compounds.

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Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians (Preprint)

10.2196/preprints.14232 ◽

2019 ◽

Author(s):

Sania Safdar Butt ◽

Yasmin Badshah ◽

Maria Shabbir ◽

Mehak Rafiq

Keyword(s):

Molecular Docking ◽

San Francisco ◽

Target Protein ◽

Autodock Vina ◽

Protein Database ◽

Computational Docking ◽

Chemical Systems ◽

Modern Drug ◽

User Friendly ◽

Ucsf Chimera

UNSTRUCTURED In the field of drug discovery, many methods of molecular modeling have been employed to study complex biological and chemical systems. Experimental strategies are integrated with computational approaches for the identification, characterization, and development of novel drugs and compounds. In modern drug designing, molecular docking is an approach that explores the confirmation of a ligand within the binding site of a macromolecule. To date, many software and tools for docking have been employed. AutoDock Vina (in UCSF [University of California, San Francisco] Chimera) is one of the computationally fastest and most accurate software employed in docking. In this paper, a sequential demonstration of molecular docking of the ligand fisetin with the target protein Akt has been provided, using AutoDock Vina in UCSF Chimera 1.12. The first step involves target protein ID retrieval from the protein database, the second step involves visualization of the protein structure in UCSF Chimera, the third step involves preparation of the target protein for docking, the fourth step involves preparation of the ligand for docking, the fifth step involves docking of the ligand and the target protein as Mol.2 files in Chimera by using AutoDock Vina, and the final step involves interpretation and analysis of the docking results. By following the guidelines and steps outlined in this paper, researchers with no previous background in bioinformatics research can perform computational docking in an easier and more user-friendly manner.

Download Full-text