Academic literature on the topic 'AUTODOCK4'

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Journal articles on the topic "AUTODOCK4"

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Valencia, Eduvan, Mauricio Galvis, Jorge Nisperuza, Vladimir Ballesteros, and Fredy Mesa. "In Silico Evaluation of Potential NDM-1 Inhibitors: An Integrated Docking and Molecular Dynamics Approach." Pharmaceuticals 17, no. 12 (2024): 1715. https://doi.org/10.3390/ph17121715.

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Background/Objectives: Non-fermenting Gram-negative bacteria are resistant to most antibiotics, due to the production of enzymes such as NDM-1. Faced with this challenge, computational methods have become essential for the design of NDM-1 carbapenemase inhibitors, optimizing both the time and cost of the development of new lead molecules. Methods: In this study, molecular docking and molecular dynamics (MD) simulations were performed in order to identify effective inhibitors against the NDM-1 enzyme. Protein preparation was carried out using UCSF Chimera and AutoDockTools 1.5.7, while ligands
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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.

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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
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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.

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Casbarra, Lorenzo, and Piero Procacci. "Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges." Journal of Computer-Aided Molecular Design 35, no. 6 (2021): 721–29. http://dx.doi.org/10.1007/s10822-021-00388-4.

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AbstractWe systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6, SAMPL7 and SAMPL8 challenges. We found that Autodock4 behaves surprisingly well, outperforming in many instances expensive molecular dynamics or quantum chemistry techniques, with an extremely favorable benefit-cost ratio. Some interesting features of Autodock4 predictions are revealed, yielding valuable hints on the overall reliability of docking screening campaigns in drug discovery projects.
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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.

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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
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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.

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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
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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.

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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
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Morris, Garrett M., Ruth Huey, William Lindstrom, et al. "AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility." Journal of Computational Chemistry 30, no. 16 (2009): 2785–91. http://dx.doi.org/10.1002/jcc.21256.

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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.

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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
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Belhocine, Youghourta, Seyfeddine Rahali, Hamza Allal, Ibtissem Meriem Assaba, Monira Galal Ghoniem та Fatima Adam Mohamed Ali. "A Dispersion Corrected DFT Investigation of the Inclusion Complexation of Dexamethasone with β-Cyclodextrin and Molecular Docking Study of Its Potential Activity against COVID-19". Molecules 26, № 24 (2021): 7622. http://dx.doi.org/10.3390/molecules26247622.

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The encapsulation mode of dexamethasone (Dex) into the cavity of β-cyclodextrin (β-CD), as well as its potential as an inhibitor of the COVID-19 main protease, were investigated using density functional theory with the recent dispersion corrections D4 and molecular docking calculations. Independent gradient model and natural bond orbital approaches allowed for the characterization of the host–guest interactions in the studied systems. Structural and energetic computation results revealed that hydrogen bonds and van der Waals interactions played significant roles in the stabilization of the for
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Dissertations / Theses on the topic "AUTODOCK4"

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Cisse, Cheickna. "Etude structurale des aptamères peptidiques anti-Fur et de leur interaction avec leur cible." Phd thesis, Université de Grenoble, 2012. http://tel.archives-ouvertes.fr/tel-00846781.

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Fur (Ferric Uptake Regulator) est un régulateur transcriptionnel spécifique des bactéries qui intervient dans le contrôle de l'homéostasie du fer, ce qui en fait une cible antibactérienne intéressante. Avant mon arrivée au laboratoire, quatre inhibiteurs interagissant spécifiquement avec Fur avaient été isolés. La partie active de ces inhibiteurs consiste en des peptides de 13 acides aminés. Au cours de cette thèse, j'ai utilisé une double-approche : théorique et expérimentale pour étudier l'interaction de ces peptides avec Fur afin de comprendre le mécanisme d'inhibition. J'ai synthétisé plus
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Wang, Qi. "Protein-ligand Docking Application and Comparison using Discovery Studio and AutoDock." Thesis, North Dakota State University, 2017. https://hdl.handle.net/10365/28365.

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Protein-ligand docking is a structure-based computational method, which is used to predict the small molecule binding modes and binding affinities with protein receptors. The goals of this study are to compare the docking performances of different software and apply the docking method to predict how protein fatty acid desaturase 1 (FADS1) interact with ligands. Two docking software, Discovery Studio and AutoDock, are used for docking comparison of 195 protein-ligand complexes from PDBind dataset. AutoDock performs a little bit better than Discovery Studio on the docking percentage, which is th
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Nadas, Janos Istvan. "Computational Structure Activity Relationship Studies on the CD1d/Glycolipid/TCR Complex using AMBER and AUTODOCK." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1251145085.

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Jesus, Éverton Mendonça de. "Adaptação e avaliação de triagem virtual em arquiteturas paralelas híbridas." Instituto de Matemática. Departamento de Ciência da Computação, 2016. http://repositorio.ufba.br/ri/handle/ri/22716.

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Submitted by Mayara Nascimento (mayara.nascimento@ufba.br) on 2017-05-31T11:34:12Z No. of bitstreams: 1 dissertacao-everton-mendonca Copy.pdf: 756322 bytes, checksum: 010382d1618c37e3db7570c6c156e7fa (MD5)<br>Approved for entry into archive by Vanessa Reis (vanessa.jamile@ufba.br) on 2017-06-02T14:02:16Z (GMT) No. of bitstreams: 1 dissertacao-everton-mendonca Copy.pdf: 756322 bytes, checksum: 010382d1618c37e3db7570c6c156e7fa (MD5)<br>Made available in DSpace on 2017-06-02T14:02:16Z (GMT). No. of bitstreams: 1 dissertacao-everton-mendonca Copy.pdf: 756322 bytes, checksum: 010382d1618c37e3db7570
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DI, DOMIZIO ALESSANDRO. "Development of methodologies for molecular docking and their applications." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2009. http://hdl.handle.net/10281/7460.

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Virtual High Throughput Screening (vHTS) has an increasingly important role in lowering both costs and time in drug discovery. The present work deals with the development (C++ programming language) of a new molecular docking software (semi-flexible model) to be used for vHTS. It would improve some of the main aspects of this type of softwares in current use, with particular reference to the program AutoDock: a particular importance is given to the calculation of the ligand conformational energy variation in passing from the unbound to the bound state, which represents a crucial term in the doc
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Ghiasi, Zahra. "Development of a Computational Mechanism to Generate Molecules with Drug-likeCharacteristics." Ohio University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou162861276157897.

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Österberg, Fredrik. "Exploring Ligand Binding in HIV-1 Protease and K+ Channels Using Computational Methods." Doctoral thesis, Uppsala universitet, Strukturell molekylärbiologi, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6167.

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Understanding protein-ligand interactions is highly important in drug development. In the present work the objective is to comprehend the link between structure and function using molecular modelling. Specifically, this thesis has been focused on implementation of receptor flexibility in molecular docking and studying structure-activity relationships of potassium ion channels and their blockers. In ligand docking simulations protein motion and heterogeneity of structural waters are approximated using an ensemble of protein structures. Four methods of combining multiple target structures within
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Chen, Sih-Yu. "Computational studies of biomolecules." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/11064.

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In modern drug discovery, lead discovery is a term used to describe the overall process from hit discovery to lead optimisation, with the goal being to identify drug candidates. This can be greatly facilitated by the use of computer-aided (or in silico) techniques, which can reduce experimentation costs along the drug discovery pipeline. The range of relevant techniques include: molecular modelling to obtain structural information, molecular dynamics (which will be covered in Chapter 2), activity or property prediction by means of quantitative structure activity/property models (QSAR/QSPR), wh
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Tiwari, Rohit. "COMPUTATIONAL AND SYNTHETIC STUDIES ON ANTIMETABOLITES FOR ANTICANCER-, ANTIVIRAL-,AND ANTIBIOTIC DRUG DISCOVERY." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1267819591.

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邱姿蓉. "A docking study of complexes of colchicine binding site ligands and tubulin using autodock." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/36911874494563401848.

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Books on the topic "AUTODOCK4"

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Steve, Beats, Nesbitt Bryce, and Commodore-Amiga Inc, eds. Amiga ROM kernel reference manual: Includes and autodocs. Addison-Wesley, 1989.

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Patel, Rajesh, and Vishal Mevada. Beginner`s Guide to Protein- Ligand Docking Using Autodock Vina: HOW to DOCK in 3 EASY STEPS USING AUTODOCK VINA Concise Guide to Docking. Independently Published, 2017.

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Commodore-Amiga, Inc. Amiga Rom Kernel Reference Manual: Includes and Autodocs (Amiga Technical Reference Series). Addison-Wesley (C), 1991.

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Book chapters on the topic "AUTODOCK4"

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Bitencourt-Ferreira, Gabriela, Val Oliveira Pintro, and Walter Filgueira de Azevedo. "Docking with AutoDock4." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9752-7_9.

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Hill, Anthony D., and Peter J. Reilly. "Scoring Functions for AutoDock." In Methods in Molecular Biology. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2343-4_27.

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Hart, William E., Chris Rosin, Richard K. Belew, and Garrett M. Morris. "Improved Evolutionary Hybrids for Flexible Ligand Docking in AutoDock." In Nonconvex Optimization and Its Applications. Springer US, 2000. http://dx.doi.org/10.1007/978-1-4757-3218-4_12.

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Yang, Zhangfan, Kun Cao, Junkai Ji, Zexuan Zhu, and Jianqiang Li. "Adopting Autodock Koto for Virtual Screening of COVID-19." In Lecture Notes in Computer Science. Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-4749-2_64.

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Schieffer, Gabin, and Ivy Peng. "Accelerating Drug Discovery in AutoDock-GPU with Tensor Cores." In Euro-Par 2023: Parallel Processing. Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-39698-4_41.

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Varela-Salinas, Génesis, Carlos Armando García-Pérez, Rafael Peláez, and Adolfo J. Rodríguez. "Visual Clustering Approach for Docking Results from Vina and AutoDock." In Lecture Notes in Computer Science. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-59650-1_29.

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Kashid, Snehal, Ashish Suttee, and Prasad Kadam. "In Silico Prediction and Screening of Potential Immunomodulators Using Autodock Vina." In Techno-Societal 2022. Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-34648-4_57.

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Liu, Zhuoran, Changsheng Zhang, Qidong Zhao, Bin Zhang, and Wenjuan Sun. "Comparative Study of Evolutionary Algorithms for Protein-Ligand Docking Problem on the AutoDock." In Simulation Tools and Techniques. Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-32216-8_58.

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K, Rohini, and Shanthi V. "Receptor Cavity-Based Approach Combined with Autodock Protocol for the Screening of Antiviral Compounds from Streptomyces sp." In Methods in Actinobacteriology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-1728-1_39.

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El-Hachem, Nehme, Benjamin Haibe-Kains, Athar Khalil, Firas H. Kobeissy, and Georges Nemer. "AutoDock and AutoDockTools for Protein-Ligand Docking: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1(BACE1) as a Case Study." In Methods in Molecular Biology. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6952-4_20.

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Conference papers on the topic "AUTODOCK4"

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Lonika, Charistika, Dono Indarto, and Amelya Augusthina Ayusari. "Roseoside from Lemon Fruits (<i>Citrus limon)</i> as a Potential Inhibitor of Cluster of Differentiation 36 for Obesity Treatment." In 8th International Conference on Advanced Material for Better Future. Trans Tech Publications Ltd, 2025. https://doi.org/10.4028/p-vo3mlu.

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Obesity is a global health problem that prevalence has increased in the last decade. Triglycerides are the main fat component in daily food intake, which can be absorbed directly into the enterocytes through Cluster of Differentiation (CD) 36 transporter protein. Glucagon-like peptide 1 receptor agonist (semaglutide) has recently been approved for obesity treatment, but this medicine has some side effects in the gastrointestinal tract. Administration of Lactobacillus-fermented lemon juice reduced serum triglyceride levels and body weight (BW) of obese rats but it is not related to the action o
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Alsawaf, Shahed, Tuğba Bal, and Zihni Onur Çalışkaner. "EXPLORING THE POTENTIAL OF DRUG REPURPOSING AGAINST ABNORMALLY REGULATED CELL-MATRIX INTERACTIONS IN THE TREATMENT OF PANCREATIC CANCER (A COMPUTATIONAL STUDY)." In STRA International Conference on Engineering & Technology, 09-10 October 2024, Istanbul. Global Research & Development Services, 2024. https://doi.org/10.20319/icstr.2024.9192.

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Pancreatic ductal adenocarcinoma (PDAC) represents one of the most aggressive cancers, with a 5-year survival rate of only 8%. The progression of the disease is significantly influenced by the tumor microenvironment, especially by cell-extracellular matrix (ECM) interactions. The aim of this study is to repurpose small molecules as inhibitor candidates to jointly target key receptors for the ECM attachment, specifically discoidin domain receptors (DDR1 and DDR2), which are implicated in promoting tumor growth through cell-collagen interactions.Using a computational drug repurposing framework,
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Kannan, Sarnath, and Raghavendra Ganji. "Porting Autodock to CUDA." In 2010 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2010. http://dx.doi.org/10.1109/cec.2010.5586277.

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Rakhshani, Hojjat, Lhassane Idoumghar, Julien Lepagnot, Mathieu Brevilliers, and Edward Keedwell. "Automatic hyperparameter selection in Autodock." In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2018. http://dx.doi.org/10.1109/bibm.2018.8621172.

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Hisle, Mark S., Maxwell S. Meier, and David M. Toth. "Accelerating AutoDock Vina with Containerization." In PEARC '18: Practice and Experience in Advanced Research Computing. ACM, 2018. http://dx.doi.org/10.1145/3219104.3219154.

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Solis-Vasquez, Leonardo, Diogo Santos-Martins, Andreas Koch, and Stefano Forli. "Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking." In 2020 28th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP). IEEE, 2020. http://dx.doi.org/10.1109/pdp50117.2020.00031.

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Lang Yu, Zhongzhi Luan, Xiangzheng Sun, Zhe Wang, and Hailong Yang. "VinaSC: Scalable Autodock Vina with fine-grained scheduling on heterogeneous platform." In 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2016. http://dx.doi.org/10.1109/bibm.2016.7822624.

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Damayanti, Sophi, Andhika Bintang Mahardhika, Slamet Ibrahim, Wei Lim Chong, Vannajan Sanghiran Lee, and Daryono Hadi Tjahjono. "O-desmethylquinine as a cyclooxygenase-2 (COX-2) inhibitors using AutoDock Vina." In 3RD INTERNATIONAL CONFERENCE ON FUNDAMENTAL AND APPLIED SCIENCES (ICFAS 2014): Innovative Research in Applied Sciences for a Sustainable Future. AIP Publishing LLC, 2014. http://dx.doi.org/10.1063/1.4898452.

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Babu, M. Naresh, R. Bhramaramba, and Allam Appa Rao. "Structure based drug design studies on urokinase plasminogen activator inhibitors using AutoDock." In the Second International Conference. ACM Press, 2012. http://dx.doi.org/10.1145/2393216.2393301.

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Srinivasu, Nulaka, K. V. V. Satyanarayana, and N. Gopala Krishna Murthy. "Structure based drug design studies on CDK2 amino pyrazole inhibitors using Autodock Tools." In 2014 Conference on IT in Business, Industry and Government (CSIBIG). IEEE, 2014. http://dx.doi.org/10.1109/csibig.2014.7056965.

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