Log in

Relevant bibliographies by topics / Autodock / Journal articles

To see the other types of publications on this topic, follow the link: Autodock.

Journal articles on the topic 'Autodock'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 50 journal articles for your research on the topic 'Autodock.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

1

Tanisa, Asti Anna, and Rezi Riadhi. "VIRTUAL SCREENING OF BETA-SECRETASE 1 (BACE1) INHIBITORS IN THE INDONESIAN HERBAL DATABASE AS USING AUTODOCK AND AUTODOCK VINA." Asian Journal of Pharmaceutical and Clinical Research 10, no. 17 (2017): 148. http://dx.doi.org/10.22159/ajpcr.2017.v10s5.23119.

Full text

Abstract:

Objective: Alzheimer’s is a neurodegenerative disease caused by the accumulation of senile plaque in the brain that affects neuronal system leading to a less sensitive cellular response from neurons. Previous research has found that beta-secretase 1 (BACE1) plays an important role in the senile plaque formation, become a target in Alzheimer’s medication.Methods: In this study, virtual screening of BACE1 inhibitors on the Indonesian Herbal Database was done using AutoDock and AutoDock Vina. The screening was validated using the directory of useful decoys: Enhanced database. Parameters for valid

APA, Harvard, Vancouver, ISO, and other styles

2

Sarthak, Pal1 Meenu Chaudhary*2 Kanishak Kala3. "Autodock & Autodock Vina: Development, Capabilities, & Applications in Molecular Docking." International Journal of Pharmaceutical Sciences 3, no. 5 (2025): 3005–19. https://doi.org/10.5281/zenodo.15458275.

Full text

Abstract:

AutoDock and AutoDock Vina are popular molecular docking technologies that are essential to structure-based drug discovery because they can predict ligand-receptor interactions. Their theoretical underpinnings, methods of application, and comparative effectiveness across several biological targets are assessed in this study. Vina's multicore support and empirical scoring are compared to AutoDock4's semi-empirical scoring function and flexible docking strategy. Furthermore, the impact of developments like AutoGridFR and GPU-accelerated versions on computational efficiency is examined. The benef

APA, Harvard, Vancouver, ISO, and other styles

3

Arcon, Juan Pablo, Carlos P. Modenutti, Demian Avendaño, et al. "AutoDock Bias: improving binding mode prediction and virtual screening using known protein–ligand interactions." Bioinformatics 35, no. 19 (2019): 3836–38. http://dx.doi.org/10.1093/bioinformatics/btz152.

Full text

Abstract:

Abstract Summary The performance of docking calculations can be improved by tuning parameters for the system of interest, e.g. biasing the results towards the formation of relevant protein–ligand interactions, such as known ligand pharmacophore or interaction sites derived from cosolvent molecular dynamics. AutoDock Bias is a straightforward and easy to use script-based method that allows the introduction of different types of user-defined biases for fine-tuning AutoDock4 docking calculations. Availability and implementation AutoDock Bias is distributed with MGLTools (since version 1.5.7), and

APA, Harvard, Vancouver, ISO, and other styles

4

Flores, Doménica, and Carola Jerves. "Computational Comparison of the Binding Affinity of Selective and Nonselective NSAIDs to COX-2 Using Molecular Docking." Bionatura Journal 2, no. 2 (2025): 1–14. https://doi.org/10.70099/bj/2025.02.02.3.

Full text

Abstract:

Cyclooxygenase-2 (COX-2) plays a key role in inflammation, making it a prime target for nonsteroidal anti-inflammatory drugs (NSAIDs). This study uses molecular docking to compare the binding affinities of four nonselective NSAIDs (aspirin, ibuprofen, diclofenac, naproxen) and three selective COX-2 inhibitors (celecoxib, rofecoxib, etoricoxib) to COX-2. Simulations with AutoDock4 and AutoDock Vina revealed distinct differences in binding profiles and selectivity. Selective COX-2 inhibitors exhibited stronger binding affinities, with etoricoxib achieving -11.22 kcal/mol (AutoDock4), driven by k

APA, Harvard, Vancouver, ISO, and other styles

5

Nguyen, Nguyen Thanh, Trung Hai Nguyen, T. Ngoc Han Pham, et al. "Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity." Journal of Chemical Information and Modeling 60, no. 1 (2019): 204–11. http://dx.doi.org/10.1021/acs.jcim.9b00778.

Full text

APA, Harvard, Vancouver, ISO, and other styles

6

Gaillard, Thomas. "Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark." Journal of Chemical Information and Modeling 58, no. 8 (2018): 1697–706. http://dx.doi.org/10.1021/acs.jcim.8b00312.

Full text

APA, Harvard, Vancouver, ISO, and other styles

7

Tang, Shidi, Ruiqi Chen, Mengru Lin, et al. "Accelerating AutoDock Vina with GPUs." Molecules 27, no. 9 (2022): 3041. http://dx.doi.org/10.3390/molecules27093041.

Full text

Abstract:

AutoDock Vina is one of the most popular molecular docking tools. In the latest benchmark CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best docking power among all the docking tools. Modern drug discovery is facing a common scenario of large virtual screening of drug hits from huge compound databases. Due to the seriality characteristic of the AutoDock Vina algorithm, there is no successful report on its parallel acceleration with GPUs. Current acceleration of AutoDock Vina typically relies on the stack of computing power as well as the allocation of resourc

APA, Harvard, Vancouver, ISO, and other styles

8

Tanchuk, Vsevolod, Volodymyr Tanin, Andriy Vovk, and Gennady Poda. "A New Scoring Function for Molecular Docking Based on AutoDock and AutoDock Vina." Current Drug Discovery Technologies 12, no. 3 (2015): 170–78. http://dx.doi.org/10.2174/1570163812666150825110208.

Full text

APA, Harvard, Vancouver, ISO, and other styles

9

Goodsell, David S., Michel F. Sanner, Arthur J. Olson, and Stefano Forli. "The AutoDock suite at 30." Protein Science 30, no. 1 (2020): 31–43. http://dx.doi.org/10.1002/pro.3934.

Full text

APA, Harvard, Vancouver, ISO, and other styles

10

Salamah, Nabilah Nurtika, Widya Dwi Aryati, and Arry Yanuar. "Virtual Screening of Indonesian Herbal Database as Adenosine A2A Antagonist using AutoDock and AutoDock Vina." Pharmacognosy Journal 11, no. 6 (2019): 1219–24. http://dx.doi.org/10.5530/pj.2019.11.189.

Full text

APA, Harvard, Vancouver, ISO, and other styles

11

Ivonie, Ulfa, Arry Yanuar, and Firdayani . "VIRTUAL SCREENING OF INDONESIAN HERBAL DATABASE FOR CP ALLOSTERIC MODULATOR OF HEPATITIS B VIRUS." International Journal of Applied Pharmaceutics 10, no. 1 (2018): 190. http://dx.doi.org/10.22159/ijap.2018.v10s1.42.

Full text

Abstract:

Objective: This study performed a virtual screening of the Indonesian Herbal Database for the core protein allosteric modulator of the hepatitis Bvirus (HBV) using AutoDock and AutoDock Vina software, to discover novel safe drugs for patients.Methods: The method was validated using the parameters enrichment factor (EF), receiver operating characteristics, and area under the curve (AUC).The grid box size used in virtual screening with AutoDock was 55 × 55 × 55 with EF10% of 0.7652 and AUC of 0.6709, whereas that used in virtualscreening with AutoDock Vina was 20.625 × 20.625 × 20.625 with EF5%

APA, Harvard, Vancouver, ISO, and other styles

12

Vieira, Tatiana F., and Sérgio F. Sousa. "Comparing AutoDock and Vina in Ligand/Decoy Discrimination for Virtual Screening." Applied Sciences 9, no. 21 (2019): 4538. http://dx.doi.org/10.3390/app9214538.

Full text

Abstract:

AutoDock and Vina are two of the most widely used protein–ligand docking programs. The fact that these programs are free and available under an open source license, also makes them a very popular first choice for many users and a common starting point for many virtual screening campaigns, particularly in academia. Here, we evaluated the performance of AutoDock and Vina against an unbiased dataset containing 102 protein targets, 22,432 active compounds and 1,380,513 decoy molecules. In general, the results showed that the overall performance of Vina and AutoDock was comparable in discriminating

APA, Harvard, Vancouver, ISO, and other styles

13

Istyastono, Enade Perdana. "DOCKING STUDIES OF CURCUMIN AS A POTENTIAL LEAD COMPOUND TO DEVELOP NOVEL DIPEPTYDYL PEPTIDASE-4 INHIBITORS." Indonesian Journal of Chemistry 9, no. 1 (2010): 132–36. http://dx.doi.org/10.22146/ijc.21574.

Full text

Abstract:

Interaction of curcumin to dipeptydyl peptidase-4 (DPP-4) has been studied by employing docking method using Molecular Operating Environment (MOE) and AutoDock as the docking software applications. Although MOE can sample more conformational spaces that represent the original interaction poses than AutoDock, both softwares serve as valid and acceptable docking applications to study the interactions of small compound to DPP-4. The calculated free energy of binding (DGbinding) results from MOE and AutoDock shows that curcumin is needed to be optimized to reach similar or better DGbinding compare

APA, Harvard, Vancouver, ISO, and other styles

14

Tanchuk, Vsevolod Yu, Volodymyr O. Tanin, Andriy I. Vovk, and Gennady Poda. "A New, Improved Hybrid Scoring Function for Molecular Docking and Scoring Based on AutoDock and AutoDock Vina." Chemical Biology & Drug Design 87, no. 4 (2015): 618–25. http://dx.doi.org/10.1111/cbdd.12697.

Full text

APA, Harvard, Vancouver, ISO, and other styles

15

Lestari, Ayu Rahmania, Irmanida Batubara, Setyanto Tri Wahyudi, and Auliya Ilmiawati. "Phenolic Compound in Garlic (Allium sativum) and Black Garlic Potency as Antigout Using Molecular Docking Approach." Jurnal Kimia Sains dan Aplikasi 25, no. 7 (2022): 253–63. http://dx.doi.org/10.14710/jksa.25.7.253-263.

Full text

Abstract:

Phenolics, including flavonoids, are bioactive components in garlic in relatively abundant amounts and are present 2–4 times more in black garlic. Both of these compounds are reported to have biological activity, with one of them acting as an antioxidant. However, its ability as an antigout is still not widely reported. Xanthine oxidase, adenine deaminase, guanine deaminase, purine nucleoside phosphorylase, and 5-Nucleotidase II are involved during the production of uric acid and causes gout. This study predicted the potential of the phenolic and flavonoid compounds in garlic and black garlic

APA, Harvard, Vancouver, ISO, and other styles

16

Suwardi, Suwardi, Agus Salim, Raden Rara Fadhila Kirana Nugrahani, and Yolanda Amalia. "Molecular Docking and Dynamics Simulation for Searching Anti-Cancer Compounds of Piperlongumine Derivatives that Have Potential as an Inhibitor Against MAO-B (Monoamine Oxidase B)." Indonesian Journal of Chemistry and Environment 6, no. 1 (2023): 18–28. http://dx.doi.org/10.21831/ijoce.v6i1.61429.

Full text

Abstract:

The docking of the piperlongumine molecule and its derivatives has been carried out to find molecules that have the potential as anti-cancer. A total of 18 ligands were docked to the 2v5z protein using the autodock4 and autodock vina programs. The binding energies of piperlongumine and piperlongumine derivatives [R1 = CH3 and R2 = H] were -8.6 kcal/mol and -9.3 kcal/mol, respectively. Based on molecular dynamics simulations, the hydrogen bond interaction fraction was dominated by GLN 206 residue in both the SAG (88%) and piperlongumine derivatives ((R1=CH3, R2 = H)(93%) ligand, for this reason

APA, Harvard, Vancouver, ISO, and other styles

17

Cosconati, Sandro, Stefano Forli, Alex L. Perryman, Rodney Harris, David S. Goodsell, and Arthur J. Olson. "Virtual screening with AutoDock: theory and practice." Expert Opinion on Drug Discovery 5, no. 6 (2010): 597–607. http://dx.doi.org/10.1517/17460441.2010.484460.

Full text

APA, Harvard, Vancouver, ISO, and other styles

18

Zhang, Yuqi, and Michel F. Sanner. "Docking Flexible Cyclic Peptides with AutoDock CrankPep." Journal of Chemical Theory and Computation 15, no. 10 (2019): 5161–68. http://dx.doi.org/10.1021/acs.jctc.9b00557.

Full text

APA, Harvard, Vancouver, ISO, and other styles

19

Goodsell, D. S. "Computational Docking of Biomolecular Complexes with AutoDock." Cold Spring Harbor Protocols 2009, no. 5 (2009): pdb.prot5200. http://dx.doi.org/10.1101/pdb.prot5200.

Full text

APA, Harvard, Vancouver, ISO, and other styles

20

Xue, Qiao, Xian Liu, Paul Russell, et al. "Evaluation of the binding performance of flavonoids to estrogen receptor alpha by Autodock, Autodock Vina and Surflex-Dock." Ecotoxicology and Environmental Safety 233 (March 2022): 113323. http://dx.doi.org/10.1016/j.ecoenv.2022.113323.

Full text

APA, Harvard, Vancouver, ISO, and other styles

21

Pratama, M. R. F., and S. Siswandono. "NUMBER OF RUNS VARIATIONS ON AUTODOCK 4 DO NOT HAVE A SIGNIFICANT EFFECT ON RMSD FROM DOCKING RESULTS." Pharmacy & Pharmacology 8, no. 6 (2021): 476–80. http://dx.doi.org/10.19163/2307-9266-2020-8-6-476-480.

Full text

Abstract:

The aim. The number of runs in the docking process with AutoDock 4 is known to play an important role in the validity of the results obtained. The greater the number of runs it is often associated with the more valid docking results. However, it is not known exactly how the most ideal runs in the docking process with AutoDock 4. This study aims to determine the effect of the number of runs docking processes with AutoDock 4 on the validity of the docking results.Materials and methods. The method used is the redocking process with AutoDock 4.2.6. The receptor used is an estrogen receptor with li

APA, Harvard, Vancouver, ISO, and other styles

22

Lu, Qiangna, Lian-Wen Qi, and Jinfeng Liu. "Improving protein–ligand binding prediction by considering the bridging water molecules in Autodock." Journal of Theoretical and Computational Chemistry 18, no. 05 (2019): 1950027. http://dx.doi.org/10.1142/s0219633619500275.

Full text

Abstract:

Water plays a significant role in determining the protein–ligand binding modes, especially when water molecules are involved in mediating protein–ligand interactions, and these important water molecules are receiving more and more attention in recent years. Considering the effects of water molecules has gradually become a routine process for accurate description of the protein–ligand interactions. As a free docking program, Autodock has been most widely used in predicting the protein–ligand binding modes. However, whether the inclusion of water molecules in Autodock would improve its docking p

APA, Harvard, Vancouver, ISO, and other styles

23

Reznichenko, Liliia V. "ПРОГРАМА AUTODOCK VINA ЯК ЗАСІБ НАВЧАННЯ МАЙБУТНІХ УЧИТЕЛІВ ПРИРОДНИЧИХ ДИСЦИПЛІН". Information Technologies and Learning Tools 38, № 6 (2013): 149–61. http://dx.doi.org/10.33407/itlt.v38i6.928.

Full text

Abstract:

Стаття присвячена проблемі впровадження засобів комп’ютерних технологій у процес навчання майбутніх учителів природничих дисциплін, зокрема учителів хімії. Обґрунтовано важливість комп’ютерного моделювання під час дослідження хімічних процесів і явищ. Висвітлено особливості процесу молекулярного докінгу, як одного з методів комп’ютерного моделювання. Запропонована програма для молекулярного докінгу AutoDock Vina розглядається як засіб підвищення ефективності навчання майбутніх учителів хімії. Окреслено теоретичні положення і запропоновано практичні рекомендації щодо формування у студентів нави

APA, Harvard, Vancouver, ISO, and other styles

24

H.N., Thao,, De, T.Q., Hue, B.T.B., et al. "Docking belinostat into HDAC 8 using autodock tool." Can Tho University Journal of Science Vol.12(2) (2020): 1. http://dx.doi.org/10.22144/ctu.jen.2020.009.

Full text

APA, Harvard, Vancouver, ISO, and other styles

25

Wojciechowski, Marek. "Simplified AutoDock force field for hydrated binding sites." Journal of Molecular Graphics and Modelling 78 (November 2017): 74–80. http://dx.doi.org/10.1016/j.jmgm.2017.09.016.

Full text

APA, Harvard, Vancouver, ISO, and other styles

26

Goodsell, David S., Garrett M. Morris, and Arthur J. Olson. "Automated docking of flexible ligands: Applications of autodock." Journal of Molecular Recognition 9, no. 1 (1996): 1–5. http://dx.doi.org/10.1002/(sici)1099-1352(199601)9:1<1::aid-jmr241>3.0.co;2-6.

Full text

APA, Harvard, Vancouver, ISO, and other styles

27

Santoso, Broto. "DOCKING ANALOG KURKUMIN TURUNAN PIPERAZINDION DENGAN TUBULIN (1TUB) RANTAI  MENGGUNAKAN VINA DAN AUTODOCK1." Pharmacon: Jurnal Farmasi Indonesia 12, no. 1 (2015): 14–18. http://dx.doi.org/10.23917/pharmacon.v12i1.43.

Full text

Abstract:

Program Autodock mampu memprediksi energi bebas dan konformasi ikatan antara fleksibel ligan dan makromolekul target yang telah diketahui. Senyawa turunan dan analog kurkumin adalah ligan yang telah banyak dihasilkan dan diuji aktivitasnya. Beberapa diantaranya memiliki khasiat yang lebih baik dari kurkumin. Enam senyawa turunan piperazindion, kurkumin, PGV-0, dan PGV-1 dihitung energi optimasi geometrinya menggunakan density functional theory (DFT) – Gaussian. Ligan hasil optimasi dicari energi ikatan ligan dengan reseptor 1TUB rantai b melalui docking menggunakan Vina dan Autodock dengan met

APA, Harvard, Vancouver, ISO, and other styles

28

MA, RUIXIN, XIUJUAN XU, LEI ZHAO, REN CAO, and QIANG FANG. "MUTUAL ARTIFICIAL BEE COLONY ALGORITHM FOR MOLECULAR DOCKING." International Journal of Biomathematics 06, no. 06 (2013): 1350038. http://dx.doi.org/10.1142/s1793524513500381.

Full text

Abstract:

Molecular docking method plays an important role on the quest of potential drug candidates, which has been proven to be a valuable tool for virtual screening. Molecular docking is commonly referred to as a parameter optimization problem. During the last decade, some optimization algorithms have been introduced, such as Lamarckian genetic algorithm (LGA) and SODOCK embedded in the AutoDock program. On the basis of the latest docking software AutoDock4.2, we present a novel docking program ABCDock, which incorporates mutual artificial bee colony (MutualABC) into AutoDock. Computer simulation res

APA, Harvard, Vancouver, ISO, and other styles

29

Sharma, Tripti. "INSILICO DOCKING APPROACH TO STUDY THE BINDING AFFINITY OF ISOFLAVONES ON THE CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR ALPHA." INDIAN DRUGS 54, no. 10 (2017): 7–15. http://dx.doi.org/10.53879/id.54.10.11152.

Full text

Abstract:

The objective of the study was to carry out docking studies of isoflavone derivatives and examine their binding efficiencies to the ligand binding domain of ERα using Autodock program. A series of isoflavone derivatives were computationally designed and optimized with the AutoDock Vina software to investigate the interactions between the target compounds and the amino acid residues of the ERα.. In silico docking studies were carried out using AutoDock Vina, based on the Lamarckian genetics algorithm principle. The results showed that all the selected isoflavones showed binding energy ranging b

APA, Harvard, Vancouver, ISO, and other styles

30

Meneses, Lorena, María Fernanda Pilaquinga, and Sebastián Cuesta H. "Modelamiento molecular de la interacción de ibuprofeno con las enzimas Ciclooxigenasa 1, 2 y el Citocromo P450 2C9." Revista Ecuatoriana de Medicina y Ciencias Biológicas 35, no. 1-2 (2017): 21–29. http://dx.doi.org/10.26807/remcb.v35i1-2.248.

Full text

Abstract:

En esta investigación, se presenta el modelamiento computacional de la interacción de ibuprofeno con las enzimas Ciclooxigenasa 1, Ciclooxigenasa 2 y Citocromo P450 2C9. El objetivo fue comprobar la aplicabilidad de métodos de acoplamiento molecular en la determinación de nuevos ligandos y la localización de sitios activos en las enzimas, asàcomo también tener un mejor entendimiento del mecanismo de acción farmacológica de ibuprofeno. Para el estudio se aplicaron métodos de dinámica molecular, para modelar la interacción de la molécula de ibuprofeno con las enzimas, determinando el sitio activ

APA, Harvard, Vancouver, ISO, and other styles

31

Ostrikova, O. I. "COMPUTER SIMULATION OF GLICOPHORIN A AND 4-METHYL-2,6-DIISOBORNILFENOL INTERACTION BY AUTODOCK AND HEXSERVER PROGRAMS." Bulletin of Siberian Medicine 13, no. 5 (2014): 62–66. http://dx.doi.org/10.20538/1682-0363-2014-5-62-66.

Full text

Abstract:

4-methyl-2,6-diisobornilphenol (dibornol) – a promising drug with a hemorheological activity. Glycophorin A is one of erythrocyte membrane proteins involved in the aggregation and possibly mediating rheological effects of dibornol.Objective: to conduct a modeling of the interaction dibornol and glycophorin A by AutoDock and HexServer programs.Material and methods. We used three-dimensional models of molecules dibornol and glycophorin A. Information on the three-dimensional model of glycophorin A was received from the database RCSB Protein Data Bank – 1AFO. Modeling the three-dimensional model

APA, Harvard, Vancouver, ISO, and other styles

32

Satpute, Uday M., and Sachin H. Rohane. "Efficiency of AUTODOCK: Insilico study of Pharmaceutical Drug Molecules." Asian Journal Of Research in Chemistry 14, no. 1 (2021): 1–5. http://dx.doi.org/10.5958/0974-4150.2021.00016.x.

Full text

APA, Harvard, Vancouver, ISO, and other styles

33

Jaghoori, Mohammad Mahdi, Boris Bleijlevens, and Silvia D. Olabarriaga. "1001 Ways to run AutoDock Vina for virtual screening." Journal of Computer-Aided Molecular Design 30, no. 3 (2016): 237–49. http://dx.doi.org/10.1007/s10822-016-9900-9.

Full text

APA, Harvard, Vancouver, ISO, and other styles

34

McElfresh, GW, and Christos Deligkaris. "A vibrational entropy term for DNA docking with autodock." Computational Biology and Chemistry 74 (June 2018): 286–93. http://dx.doi.org/10.1016/j.compbiolchem.2018.03.027.

Full text

APA, Harvard, Vancouver, ISO, and other styles

35

Bastos, Luana Luiza, and Giovana Fiorini. "Re-docking Molecular Utilizando o PyMOL e AutoDock VINA." BIOINFO 3, no. 1 (2023): 21. http://dx.doi.org/10.51780/bioinfo-03-21.

Full text

Abstract:

O tutorial a seguir aborda a técnica de re-docking utilizada como etapa inicial em simulações de docking molecular para validar a ferramenta utilizada, bem como suas funções de pontuação. O re-docking consiste em separar um complexo proteína-ligante resolvido experimentalmente e buscar encontrar uma conformação parecida através do docking. Neste tutorial utilizaremos o PyMOL como uma ferramenta visual auxiliar para o re-docking utilizando o Vina.

APA, Harvard, Vancouver, ISO, and other styles

36

LIU, YU, WENTAO LI, and RUIXIN MA. "PARTICLE SWARM OPTIMIZATION ON FLEXIBLE DOCKING." International Journal of Biomathematics 05, no. 05 (2012): 1250044. http://dx.doi.org/10.1142/s1793524511001866.

Full text

Abstract:

Molecular docking is an important tool in screening large libraries of compounds to determine the interactions between potential drugs and the target proteins. The molecular docking problem is how to locate a good conformation to dock a ligand to the large molecule. It can be formulated as a parameter optimization problem consisting of a scoring function and a global optimization method. Many docking methods have been developed with primarily these two parts varying. In this paper, a variety of particle swarm optimization (PSO) variants were introduced to cooperate with the semiempirical free

APA, Harvard, Vancouver, ISO, and other styles

37

Isaac, Arnold Emerson, Faizy Khan, Shantanu Bafna, and Tanu Gupta. "Virtual Screening of potential inhibitors from Herbs for the treatment of Breast Cancer." Asian Journal of Pharmaceutical and Clinical Research 10, no. 4 (2017): 62. http://dx.doi.org/10.22159/ajpcr.2017.v10i4.14959.

Full text

Abstract:

Objectives: Cancer is a disease which results in uncontrollable abnormal cells division and destruction of body tissues. Breast cancer occurs when malignant tumors develop in the breast. Breast cancer is the second leading cause of death among women. To study the role of herbs used in the treatment for breast cancer. To investigate the anti-breast cancer activity of compounds present on most common herbs and to analyse their interaction with amino acids in the active sites. Methods: Complementary and alternative medicine is often used for curing cancer mainly the breast cancer. Also certain st

APA, Harvard, Vancouver, ISO, and other styles

38

Macari, Gabriele, Daniele Toti, Andrea Pasquadibisceglie, and Fabio Polticelli. "DockingApp RF: A State-of-the-Art Novel Scoring Function for Molecular Docking in a User-Friendly Interface to AutoDock Vina." International Journal of Molecular Sciences 21, no. 24 (2020): 9548. http://dx.doi.org/10.3390/ijms21249548.

Full text

Abstract:

Motivation: Bringing a new drug to the market is expensive and time-consuming. To cut the costs and time, computer-aided drug design (CADD) approaches have been increasingly included in the drug discovery pipeline. However, despite traditional docking tools show a good conformational space sampling ability, they are still unable to produce accurate binding affinity predictions. This work presents a novel scoring function for molecular docking seamlessly integrated into DockingApp, a user-friendly graphical interface for AutoDock Vina. The proposed function is based on a random forest model and

APA, Harvard, Vancouver, ISO, and other styles

39

Yanuar, Arry, Rezi Riadhi Syahdi, and Widya Dwi Aryati. "PARAMETER OPTIMIZATION AND VIRTUAL SCREENING INDONESIAN HERBAL DATABASE AS HUMAN IMMUNODEFICIENCY VIRUS -1 INTEGRASE INHIBITOR USING AUTODOCK AND VINA." International Journal of Applied Pharmaceutics 9 (October 30, 2017): 90. http://dx.doi.org/10.22159/ijap.2017.v9s1.51_57.

Full text

Abstract:

Objective: Human immunodeficiency virus (HIV-1) is a virus that causes acquired immunodeficiency syndrome, a disease considered to be one of themost dangerous because of its high mortality, morbidity, and infectivity. The emergence of mutant HIV strains has led treatment to target proteaseas reverse transcriptase and integrase enzyme become less effective. This study aims to provide knowledge about the potential of HIV-1 integraseinhibitors for use as guiding compounds in the development of new anti-HIV drugs.Methods: This study used AutoDock and AutoDock Vina for virtual screening of the Indo

APA, Harvard, Vancouver, ISO, and other styles

40

Рахмонов, Б.Д., Д.А. Мансуров, У.М. Якубов та А.Х. Хаитбаев. "AUTODOCK ДАСТУРИ ЁРДАМИДА ПИКАРНОВИРУС БИЛАН ХИНАЗОЛОН-4 ҲОСИЛАЛАРИНИНГ БОҒЛАНИШИНИ ЎРГАНИШ". Educational Research in Universal Sciences 2, № 4 (2023): 951–54. https://doi.org/10.5281/zenodo.7905130.

Full text

Abstract:

Ушбу мақолада Autodock дастури ёрдамида 3-гексил хиназолон-4 нинг Пикарновирус (PDB ID: 3NKY) билан боғланиши ўрганилган. Ўрганилаётган бирикмаларнинг оқсил билан ҳосил қилган боғланиш энергиясининг (БЭ) оптимал диапазони -4.33-5.75 ккал/моль ташкил қилади.

APA, Harvard, Vancouver, ISO, and other styles

41

Marvaniya, Vanita, Hirak V. Joshi, Ujashkumar A. Shah, and Jayvadan K. Patel. "Synthesis, Anticancer Evaluation and Molecular Docking Studies of Isonicotinamide and Diaryl Urea Hybrid Motifs." Asian Journal of Organic & Medicinal Chemistry 7, no. 2 (2022): 179–86. http://dx.doi.org/10.14233/ajomc.2022.ajomc-p382.

Full text

Abstract:

In search of new anticancer agents with improved efficacy, we designed and synthesized novel hybrid series of isonicotinamide and diaryl urea motifs (R1-R9). Design of series compounds carried out using docking study by Autodock vina tool. Binding energy (more than -9.7 kcal/mol) calculated using Autodock vina against Raf kinase (PDB: 4DBN). All the synthesized compounds were evaluated for them in vitro anticancer activity against MCF-7 cell line. The anticancer activities of the synthesized compounds were also carried. Some of the compounds (R1, R8, R9) showed better activities towards MCF-7

APA, Harvard, Vancouver, ISO, and other styles

42

Butt, Sania Safdar, Yasmin Badshah, Maria Shabbir, and Mehak Rafiq. "Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians." JMIR Bioinformatics and Biotechnology 1, no. 1 (2020): e14232. http://dx.doi.org/10.2196/14232.

Full text

Abstract:

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 computat

APA, Harvard, Vancouver, ISO, and other styles

43

Reddy, K. Kumar, R. S. Rathore, P. Srujana, et al. "Performance Evaluation of Docking Programs- Glide, GOLD, AutoDock & SurflexDock, Using Free Energy Perturbation Reference Data: A Case Study of Fructose-1, 6-bisphosphatase-AMP Analogs." Mini-Reviews in Medicinal Chemistry 20, no. 12 (2020): 1179–87. http://dx.doi.org/10.2174/1389557520666200526183353.

Full text

Abstract:

Background: The accurate ranking of analogs of lead molecules with respect to their estimated binding free energies to drug targets remains highly challenging in molecular docking due to small relative differences in their free energy values. Methods: Free energy perturbation (FEP) method, which provides the most accurate relative binding free energy values were earlier used to calculate free energies of many ligands for several important drug targets including Fructose-1,6-BisphosPhatase (FBPase). The availability of abundant structural and experimental binding affinity data for FBPase inhibi

APA, Harvard, Vancouver, ISO, and other styles

44

Aldisa, Olivia, Azminah Azminah, Linda Erlina, Hayun Hayun, and Arry Yanuar. "VIRTUAL SCREENING OF INDONESIAN HERBAL DATABASE TO FIND SIRTUIN 1 ACTIVATORS USING THE DOCKING METHOD." Asian Journal of Pharmaceutical and Clinical Research 10, no. 17 (2017): 158. http://dx.doi.org/10.22159/ajpcr.2017.v10s5.23121.

Full text

Abstract:

Objective: Chemical compounds in plants often have benefits and efficacy that can be useful for medicine. Biochemistry and biomedicine research aims to develop new drugs for degenerative human diseases such as cancer, cardiovascular diseases, and diabetes mellitus. Humans have a protein that is the key for metabolic sensors in a variety of metabolic pathways, Sirtuin 1 (SIRT1). Currently, only resveratrol, fisetin, and quercetin, which are compounds from natural ingredients, have been tested as activators of SIRT1 even though there are many chemical compounds in plants that could potentially b

APA, Harvard, Vancouver, ISO, and other styles

45

Shamsara, Jamal. "Correlation between Virtual Screening Performance and Binding Site Descriptors of Protein Targets." International Journal of Medicinal Chemistry 2018 (January 11, 2018): 1–10. http://dx.doi.org/10.1155/2018/3829307.

Full text

Abstract:

Rescoring is a simple approach that theoretically could improve the original docking results. In this study AutoDock Vina was used as a docked engine and three other scoring functions besides the original scoring function, Vina, as well as their combinations as consensus scoring functions were employed to explore the effect of rescoring on virtual screenings that had been done on diverse targets. Rescoring by DrugScore produces the most number of cases with significant changes in screening power. Thus, the DrugScore results were used to build a simple model based on two binding site descriptor

APA, Harvard, Vancouver, ISO, and other styles

46

Arakelian, Arina G., Gennady N. Chuev, and Timur V. Mamedov. "Molecular Docking of Endolysins for Studying Peptidoglycan Binding Mechanism." Molecules 29, no. 22 (2024): 5386. http://dx.doi.org/10.3390/molecules29225386.

Full text

Abstract:

Endolysins of bacteriophages, which degrade the bacterial cell wall peptidoglycan, are applicable in many industries to deal with biofilms and bacterial infections. While multi-domain endolysins have both enzymatically active and cell wall-binding domains, single-domain endolysins consist only of an enzymatically active domain, and their mechanism of peptidoglycan binding remains unexplored, for this is a challenging task experimentally. This research aimed to explore the binding mechanism of endolysins using computational approaches, namely molecular docking and bioinformatical tools, and ana

APA, Harvard, Vancouver, ISO, and other styles

47

Fu, Yi, Xiaojun Wu, Zhiguo Chen, Jun Sun, Ji Zhao, and Wenbo Xu. "A New Approach for Flexible Molecular Docking Based on Swarm Intelligence." Mathematical Problems in Engineering 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/540186.

Full text

Abstract:

Molecular docking methods play an important role in the field of computer-aided drug design. In the work, on the basis of the molecular docking program AutoDock, we present QLDock as a tool for flexible molecular docking. For the energy evaluation, the algorithm uses the binding free energy function that is provided by the AutoDock 4.2 tool. The new search algorithm combines the features of a quantum-behaved particle swarm optimization (QPSO) algorithm and local search method of Solis and Wets for solving the highly flexible protein-ligand docking problem. We compute the interaction of 23 prot

APA, Harvard, Vancouver, ISO, and other styles

48

Рахмонов, Б.Д., Д.А. Мансуров, У.М. Якубов та А.Х. Хаитбаев. "AUTODOCK ДАСТУРИ ЁРДАМИДА ЭПИЛЕПСИЯ ОҚСИЛИ БИЛАН ХИНАЗОЛОН-4 ҲОСИЛАЛАРИНИНГ БОҒЛАНИШИНИ ЎРГАНИШ". Educational Research in Universal Sciences 2, № 4 (2023): 955–58. https://doi.org/10.5281/zenodo.7905141.

Full text

Abstract:

Ушбу мақолада Autodock дастури ёрдамида 2-метил, 3-гептил хиназолон-4 нинг Эпилепсия оқсили (PDB ID: 6R82) билан боғланиши ўрганилган. Ўрганилаётган бирикмаларнинг оқсил билан ҳосил қилган боғланиш энергиясининг (БЭ) оптимал диапазони -4.95-5.42 ккал/моль ташкил қилади.

APA, Harvard, Vancouver, ISO, and other styles

49

Salih, Twana Mohsin. "A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model." Iraqi Journal of Pharmaceutical Sciences ( P-ISSN 1683 - 3597 E-ISSN 2521 - 3512) 31, no. 2 (2022): 160–68. http://dx.doi.org/10.31351/vol31iss2pp160-168.

Full text

Abstract:

Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicte

APA, Harvard, Vancouver, ISO, and other styles

50

Mahmoud, Sawsan, Doaa Samaha, Mosaad S. Mohamed, et al. "Design, Synthesis, Antitumor Activity and Molecular Docking Study of Novel 5-Deazaalloxazine Analogs." Molecules 25, no. 11 (2020): 2518. http://dx.doi.org/10.3390/molecules25112518.

Full text

Abstract:

Protein tyrosine kinases (PTKs) are the most potential therapeutic targets for cancer. Herein, we present a sound rationale for synthesis of a series of novel 2-(methylthio), 2-(substituted alkylamino), 2-(heterocyclic substituted), 2-amino, 2,4-dioxo and 2-deoxo-5-deazaalloxazine derivatives by applying structure-based drug design (SBDD) using AutoDock 4.2. Their antitumor activities against human CCRF-HSB-2, KB, MCF-7 and HeLa have been investigated in vitro. Many 5-deazaalloxazine analogs revealed high selective activities against MCF-7 tumor cell lines (IC50: 0.17–2.17 µM) over HeLa tumor

APA, Harvard, Vancouver, ISO, and other styles

We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!