Relevant bibliographies by topics / Autodock

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Autodock'

Author: Grafiati
Published: 4 June 2021
Last updated: 26 July 2025

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Journal articles on the topic "Autodock"

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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.

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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
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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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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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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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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.

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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.

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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
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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.

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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.

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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.

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Dissertations / Theses on the topic "Autodock"

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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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Дядечко, Алла Миколаївна, Алла Николаевна Дядечко, Alla Mykolaivna Diadechko, and O. Shulima. "3D graphics: autodesk maya." Thesis, Видавництво СумДУ, 2010. http://essuir.sumdu.edu.ua/handle/123456789/17883.

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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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Ludwigsson, Jonas. "Creating realistic hair in Autodesk Maya." Thesis, Högskolan i Gävle, Avdelningen för Industriell utveckling, IT och Samhällsbyggnad, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:hig:diva-14411.

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This thesis work focuses on how to create realistic looking hair using only the vanilla version of Autodesk Maya. It describes two approaches, the widely used polygon-stripe based technique and the Maya built-in nHair. It also evaluates these two approaches in terms of ease of implementation, production speed and quality of final results. The conclusion is that nHair has the potential to produce realistic looking hair but contains various bugs and is not optimized at the current stage, while the polygon-stripe based approach is robust and flexible but the realism of rendering results is heavil
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Books on the topic "Autodock"

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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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Dan, Sonnen David Vesset. Autodesk. IDC Research, 2005.

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Hurkman, Alexis Van. Autodesk Smoke Essentials: Autodesk Official Press. Wiley & Sons, Incorporated, John, 2013.

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Aubin, Paul F. Mastering Autodesk Revit Building (Autodesk Revit). Autodesk Press, 2006.

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Hurkman, Alexis Van. Autodesk Smoke Essentials: Autodesk Official Press. Wiley & Sons, Incorporated, John, 2014.

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Hurkman, Alexis Van. Autodesk Smoke Essentials: Autodesk Official Press. Wiley & Sons, Incorporated, John, 2014.

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Hurkman, Alexis Van. Autodesk Smoke Essentials: Autodesk Official Press. Wiley & Sons, Incorporated, John, 2014.

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Hurkman, Alexis Van. Autodesk Smoke Essentials: Autodesk Official Press. Wiley & Sons, Incorporated, John, 2013.

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Hurkman, Alexis Van. Autodesk Smoke Essentials: Autodesk Official Press. Sybex, 2014.

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LEAKE. Autodesk Inventor. McGraw-Hill Science/Engineering/Math, 2003.

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Book chapters on the topic "Autodock"

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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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Sendler, Ulrich. "Autodesk." In Xpert.press. Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-87898-8_17.

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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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Conference papers on the topic "Autodock"

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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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Limeira, Marianni Pereira, and Ivvy Pedrosa Cavalcante Pessôa Quintella. "Avaliação da Autodesk Construction Cloud para gestão de projetos BIM." In XX ENCONTRO NACIONAL DE TECNOLOGIA DO AMBIENTE CONSTRUÍDO. UFAL, 2024. http://dx.doi.org/10.46421/entac.v20i1.6081.

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O acesso a projetos repletos de informações, modelos federados e verificações em tempo real na indústria da construção está experimentando um crescimento significativo, impulsionado pelo incentivo à adoção da metodologia BIM (Modelagem da Informação da Construção) em âmbito global. Consequentemente, identifica-se a necessidade de uma plataforma em nuvem que possa gerenciar, permitir o acesso e integrar esses modelos BIM de maneira eficiente. Este estudo analisa a utilização da plataforma Autodesk Construction Cloud (ACC) como método de verificação e gerenciamento de projetos BIM. A ACC oferece
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Verdú, Isabel Seguí, Larisa Dunai, and Lilia Sava. "Integration of Wooclap and Autodesk© Technologies in Graphic Engineering Teaching." In 2024 IEEE 11th International Conference on E-Learning in Industrial Electronics (ICELIE). IEEE, 2024. https://doi.org/10.1109/icelie62250.2024.10814781.

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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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Reports on the topic "Autodock"

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CALS TEST NETWORK WRIGHT-PATTERSON AFB OH. Technical IGES Transfer Using: AUTODESK, Incorporated's Data, MIL-D-28000A (IGES). Quick Short Test Report. Defense Technical Information Center, 1993. http://dx.doi.org/10.21236/ada313003.

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Nguyen, Ba Nghiep, and Jin Wang. PNNL Technical Support to The Implementation of EMTA and EMTA-NLA Models in Autodesk? Moldflow? Packages. Office of Scientific and Technical Information (OSTI), 2012. http://dx.doi.org/10.2172/1060674.

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Modlo, Yevhenii O., Serhiy O. Semerikov, Pavlo P. Nechypurenko, Stanislav L. Bondarevskyi, Olena M. Bondarevska, and Stanislav T. Tolmachev. The use of mobile Internet devices in the formation of ICT component of bachelors in electromechanics competency in modeling of technical objects. [б. в.], 2019. http://dx.doi.org/10.31812/123456789/3264.

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Computer simulation of technical objects and processes is one of the components of the system of professional training of a modern electromechanics engineer. It has been established that despite the fact that mobile Internet devices (MID) are actively used by electrical engineers, the methods of using them in the process of bachelor in electromechanics training is considered only in some domestic scientific studies. The article highlights the components of the methods of using MID in the formation of the ICT component of the competence of the bachelor in electromechanics in modeling of technic
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AUTODESK INC SAN RAFAEL CA. The US Army Corps of Engineers Roadmap for Life-Cycle Building Information Modeling (BIM). Supplement 1- BIM Implementation Guide for Military Construction (MILCON) Projects Using the Autodesk Platform. Defense Technical Information Center, 2012. http://dx.doi.org/10.21236/ada576142.

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Furman, Burford, Laxmi Ramasubramanian, Shannon McDonald, et al. Solar-Powered Automated Transportation: Feasibility and Visualization. Mineta Transportation Institute, 2021. http://dx.doi.org/10.31979/mti.2021.1948.

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A solar-powered automated transportation network (ATN) connecting the North and South campuses of San José State University with three passenger stations was designed, visualized, and analyzed in terms of its energy usage, carbon offset, and cost. The study’s methodology included the use of tools and software such as ArcGIS, SketchUp, Infraworks, Sketchup, Rhinoceros, and Autodesk 3DS Max. ATN vehicle energy usage was estimated using data from the university’s Park &amp; Ride shuttle bus operation and by modeling with SUMOPy, the advanced simulation suite for the micro-traffic simulator SUMO.
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Autodesk Buzzsaw®. Purdue University, 2012. http://dx.doi.org/10.5703/1288284315827.

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