Academic literature on the topic 'Ligand to protein docking'

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

Select a source type:

Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Ligand to protein docking.'

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.

Journal articles on the topic "Ligand to protein docking"

1

Wang, Kai, Nan Lyu, Hongjuan Diao, et al. "GM-DockZn: a geometry matching-based docking algorithm for zinc proteins." Bioinformatics 36, no. 13 (2020): 4004–11. http://dx.doi.org/10.1093/bioinformatics/btaa292.

Full text
Abstract:
Abstract Motivation Molecular docking is a widely used technique for large-scale virtual screening of the interactions between small-molecule ligands and their target proteins. However, docking methods often perform poorly for metalloproteins due to additional complexity from the three-way interactions among amino-acid residues, metal ions and ligands. This is a significant problem because zinc proteins alone comprise about 10% of all available protein structures in the protein databank. Here, we developed GM-DockZn that is dedicated for ligand docking to zinc proteins. Unlike the existing doc
APA, Harvard, Vancouver, ISO, and other styles
2

Bottegoni, Giovanni. "Protein-ligand docking." Frontiers in Bioscience 16, no. 1 (2011): 2289. http://dx.doi.org/10.2741/3854.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Velesinović, Aleksandar, and Goran Nikolić. "Protein-protein interaction networks and protein-ligand docking: Contemporary insights and future perspectives." Acta Facultatis Medicae Naissensis 38, no. 1 (2021): 5–17. http://dx.doi.org/10.5937/afmnai38-28322.

Full text
Abstract:
Traditional research means, such as in vitro and in vivo models, have consistently been used by scientists to test hypotheses in biochemistry. Computational (in silico) methods have been increasingly devised and applied to testing and hypothesis development in biochemistry over the last decade. The aim of in silico methods is to analyze the quantitative aspects of scientific (big) data, whether these are stored in databases for large data or generated with the use of sophisticated modeling and simulation tools; to gain a fundamental understanding of numerous biochemical processes related, in p
APA, Harvard, Vancouver, ISO, and other styles
4

Chakraborty, Sandeep. "DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations." F1000Research 3 (June 16, 2016): 262. http://dx.doi.org/10.12688/f1000research.5145.3.

Full text
Abstract:
The ability to accurately and effectively predict the interaction between proteins and small drug-like compounds has long intrigued researchers for pedagogic, humanitarian and economic reasons. Protein docking methods (AutoDock, GOLD, DOCK, FlexX and Glide to name a few) rank a large number of possible conformations of protein-ligand complexes using fast algorithms. Previously, it has been shown that structural congruence leading to the same enzymatic function necessitates the congruence of electrostatic properties (CLASP). The current work presents a methodology for docking a ligand into a ta
APA, Harvard, Vancouver, ISO, and other styles
5

Pérez, Carlos, and Angel R. Ortiz. "Evaluation of Docking Functions for Protein−Ligand Docking." Journal of Medicinal Chemistry 44, no. 23 (2001): 3768–85. http://dx.doi.org/10.1021/jm010141r.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Ng, Marcus C. K., Simon Fong, and Shirley W. I. Siu. "PSOVina: The hybrid particle swarm optimization algorithm for protein–ligand docking." Journal of Bioinformatics and Computational Biology 13, no. 03 (2015): 1541007. http://dx.doi.org/10.1142/s0219720015410073.

Full text
Abstract:
Protein–ligand docking is an essential step in modern drug discovery process. The challenge here is to accurately predict and efficiently optimize the position and orientation of ligands in the binding pocket of a target protein. In this paper, we present a new method called PSOVina which combined the particle swarm optimization (PSO) algorithm with the efficient Broyden–Fletcher–Goldfarb–Shannon (BFGS) local search method adopted in AutoDock Vina to tackle the conformational search problem in docking. Using a diverse data set of 201 protein–ligand complexes from the PDBbind database and a ful
APA, Harvard, Vancouver, ISO, and other styles
7

Xiao, Wei, Disha Wang, Zihao Shen, Shiliang Li, and Honglin Li. "Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites." Molecules 23, no. 9 (2018): 2321. http://dx.doi.org/10.3390/molecules23092321.

Full text
Abstract:
Water molecules play an important role in modeling protein-ligand interactions. However, traditional molecular docking methods often ignore the impact of the water molecules by removing them without any analysis or keeping them as a static part of the proteins or the ligands. Hence, the accuracy of the docking simulations will inevitably be damaged. Here, we introduce a multi-body docking program which incorporates the fixed or the variable number of the key water molecules in protein-ligand docking simulations. The program employed NSGA II, a multi-objective optimization algorithm, to identif
APA, Harvard, Vancouver, ISO, and other styles
8

Aziz, Fitri Kusvila, Cantika Nukitasari, Fauziyah Ardli Oktavianingrum, Lita Windy Aryati, and Broto Santoso. "Hasil In Silico Senyawa Z12501572, Z00321025, SCB5631028 dan SCB13970547 dibandingkan Turunan Zerumbon terhadap Human Liver Glycogen Phosphorylase (1l5Q) sebagai Antidiabetes." Jurnal Kimia VALENSI 2, no. 2 (2016): 120–24. http://dx.doi.org/10.15408/jkv.v2i2.4170.

Full text
Abstract:
Abstrak Human Liver Glycogen Phosphorylase (HLGP), suatu katalis glikogen yang mengontrol pelepasan glukosa-1-fosfat glikogen dari hati. Enzim ini mempunyai peran sentral dalam luaran glukosa hati sehingga menjadi target obat antidiabetik. Kajian docking dilakukan pada komputer dengan prosesor Intel Pentium, RAM 1 GB dan Windows 7. Ligan yang digunakan adalah senyawa obat (Z12501572, Z00321025, SCB5631028 dan SCB13970547), dataset pembanding aktif glycogen phosphorylase outer dimer site (PYGL-out) dan decoysdari www.dekois.com dan turunan zerumbon. Protein dipisahkan dari ligan nativ dan semua
APA, Harvard, Vancouver, ISO, and other styles
9

Ulzurrun, Eugenia, Yorley Duarte, Esteban Perez-Wohlfeil, Fernando Gonzalez-Nilo, and Oswaldo Trelles. "PLIDflow: an open-source workflow for the online analysis of protein–ligand docking using galaxy." Bioinformatics 36, no. 14 (2020): 4203–5. http://dx.doi.org/10.1093/bioinformatics/btaa481.

Full text
Abstract:
Abstract Motivation Molecular docking is aimed at predicting the conformation of small-molecule (ligands) within an identified binding site (BS) in a target protein (receptor). Protein–ligand docking plays an important role in modern drug discovery and biochemistry for protein engineering. However, efficient docking analysis of proteins requires prior knowledge of the BS, which is not always known. The process which covers BS identification and protein–ligand docking usually requires the combination of different programs, which require several input parameters. This is furtherly aggravated whe
APA, Harvard, Vancouver, ISO, and other styles
10

Sulimov, Vladimir B., Danil C. Kutov, and Alexey V. Sulimov. "Advances in Docking." Current Medicinal Chemistry 26, no. 42 (2020): 7555–80. http://dx.doi.org/10.2174/0929867325666180904115000.

Full text
Abstract:
Background: Design of small molecules which are able to bind to the protein responsible for a disease is the key step of the entire process of the new medicine discovery. Atomistic computer modeling can significantly improve effectiveness of such design. The accurate calculation of the free energy of binding a small molecule (a ligand) to the target protein is the most important problem of such modeling. Docking is one of the most popular molecular modeling methods for finding ligand binding poses in the target protein and calculating the protein-ligand binding energy. This energy is used for
APA, Harvard, Vancouver, ISO, and other styles
More sources

Dissertations / Theses on the topic "Ligand to protein docking"

1

Genheden, Samuel. "A fast protein-ligand docking method." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-69.

Full text
Abstract:
<p>In this dissertation a novel approach to protein-ligand docking is presented. First an existing method to predict putative active sites is employed. These predictions are then used to cut down the search space of an algorithm that uses the fast Fourier transform to calculate the geometrical and electrostatic complementarity between a protein and a small organic ligand. A simplified hydrophobicity score is also calculated for each active site. The docking method could be applied either to dock ligands in a known active site or to rank several putative active sites according to their biologic
APA, Harvard, Vancouver, ISO, and other styles
2

Totrov, Maxim. "Computational studies on protein-ligand docking." Thesis, Open University, 1999. http://oro.open.ac.uk/58005/.

Full text
Abstract:
This thesis describes the development and refinement of a number of techniques for molecular docking and ligand database screening, as well as the application of these techniques to predict the structures of several protein-ligand complexes and to discover novel ligands of an important receptor protein. Global energy optimisation by Monte-Carlo minimisation in internal co-ordinates was used to predict bound conformations of eight protein-ligand complexes. Experimental X-ray crystallography structures became available after the predictions were made. Comparison with the X-ray structures showed
APA, Harvard, Vancouver, ISO, and other styles
3

Claußen, Holger. "Effizientes Protein-Ligand-Docking mit flexiblen Proteinstrukturen /." Sankt Augustin : GMD-Forschungszentrum Informationstechnik, 2001. http://www.gbv.de/dms/bs/toc/33264023X.pdf.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Oledzki, Peter Richard. "Developing a protein-ligand docking algorithm : FlexLigDock." Thesis, University of Leeds, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.435818.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Datta, Deepshikha Goddard William A. "Protein-ligand interactions : docking, design and protein conformational change /." Diss., Pasadena, Calif. : California Institute of Technology, 2003. http://resolver.caltech.edu/CaltechETD:etd-03242003-111426.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Fischer, Bernhard Karl. "High throughput simulation methods for protein ligand docking." Karlsruhe : Forschungszentrum Karlsruhe, 2007. http://d-nb.info/985070374/34.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Fischer, Bernhard Karl [Verfasser]. "High throughput simulation methods for protein ligand docking / Bernhard Karl Fischer." Karlsruhe : Forschungszentrum Karlsruhe, 2007. http://d-nb.info/985070374/34.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

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.

Full text
Abstract:
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
APA, Harvard, Vancouver, ISO, and other styles
9

Andersson, David. "Multivariate design of molecular docking experiments : An investigation of protein-ligand interactions." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-35736.

Full text
Abstract:
To be able to make informed descicions regarding the research of new drug molecules (ligands), it is crucial to have access to information regarding the chemical interaction between the drug and its biological target (protein). Computer-based methods have a given role in drug research today and, by using methods such as molecular docking, it is possible to investigate the way in which ligands and proteins interact. Despite the acceleration in computer power experienced in the last decades many problems persist in modelling these complicated interactions. The main objective of this thesis was t
APA, Harvard, Vancouver, ISO, and other styles
10

Buonfiglio, Rosa <1985&gt. "Computational strategies to include protein flexibility in Ligand Docking and Virtual Screening." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6330/.

Full text
Abstract:
The dynamic character of proteins strongly influences biomolecular recognition mechanisms. With the development of the main models of ligand recognition (lock-and-key, induced fit, conformational selection theories), the role of protein plasticity has become increasingly relevant. In particular, major structural changes concerning large deviations of protein backbones, and slight movements such as side chain rotations are now carefully considered in drug discovery and development. It is of great interest to identify multiple protein conformations as preliminary step in a screening campaign. Pr
APA, Harvard, Vancouver, ISO, and other styles
More sources

Books on the topic "Ligand to protein docking"

1

Gohlke, Holger, ed. Protein-Ligand Interactions. Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527645947.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Williams, Mark A., and Tina Daviter, eds. Protein-Ligand Interactions. Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-398-5.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Nienhaus, G. Ulrich. Protein-Ligand Interactions. Humana Press, 2005. http://dx.doi.org/10.1385/1592599125.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Daviter, Tina, Christopher M. Johnson, Stephen H. McLaughlin, and Mark A. Williams, eds. Protein-Ligand Interactions. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Helmsen, Sabine. Protein-Ligand-, Protein-Inhibitor- und Protein-Protein-Wechselwirkungen. Springer Fachmedien Wiesbaden, 2020. http://dx.doi.org/10.1007/978-3-658-30151-4.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Protein-ligand interactions: Methods and applications. 2nd ed. Humana Press, 2013.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
7

Press, Humana, ed. Protein-ligand interactions: Methods and applications. Humana Press, 2010.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
8

Ballante, Flavio, ed. Protein-Ligand Interactions and Drug Design. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1209-5.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Roterman-Konieczna, Irena, ed. Identification of Ligand Binding Site and Protein-Protein Interaction Area. Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-5285-6.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

NATO ASI/FEBS Course on DNA-Ligand Interactions: From Drugs to Proteins (1986 Abbey of Fontevraud). DNA-ligand interactions: From drugs to proteins. Plenum Press, 1987.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
More sources

Book chapters on the topic "Ligand to protein docking"

1

Slynko, Inna, Didier Rognan, and Esther Kellenberger. "Protein-Ligand Docking." In Tutorials in Chemoinformatics. John Wiley & Sons, Ltd, 2017. http://dx.doi.org/10.1002/9781119161110.ch22.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Rueda, Manuel, and Ruben Abagyan. "Embracing Protein Plasticity in Ligand Docking." In Protein-Ligand Interactions. Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527645947.ch14.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Peh, Sally Chen Woon, and Jer Lang Hong. "Protein Ligand Docking Using Simulated Jumping." In Computational Science and Its Applications -- ICCSA 2016. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-42111-7_1.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Bienstock, Rachelle J. "Solvation Methods for Protein–Ligand Docking." In Methods in Molecular Biology. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2486-8_1.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Cao, Yang, Wentao Dai, and Zhichao Miao. "Evaluation of Protein–Ligand Docking by Cyscore." In Methods in Molecular Biology. Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7756-7_12.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Kim, Chong-Min, Chung-In Won, Jae-Kwan Kim, Joonghyun Ryu, Jong Bhak, and Deok-Soo Kim. "Protein-Ligand Docking Based on Beta-Shape." In Transactions on Computational Science IX. Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-16007-3_6.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Arcon, Juan Pablo, Adrián G. Turjanski, Marcelo A. Martí, and Stefano Forli. "Biased Docking for Protein–Ligand Pose Prediction." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1209-5_3.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Bottegoni, Giovanni, Walter Rocchia, and Andrea Cavalli. "Application of Conformational Clustering in Protein–Ligand Docking." In Methods in Molecular Biology. Springer New York, 2011. http://dx.doi.org/10.1007/978-1-61779-465-0_12.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Janin, Joël. "Docking Predictions of Protein-Protein Interactions and Their Assessment: The CAPRI Experiment." In Identification of Ligand Binding Site and Protein-Protein Interaction Area. Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5285-6_5.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Kuzu, Guray, Ozlem Keskin, Attila Gursoy, and Ruth Nussinov. "Expanding the Conformational Selection Paradigm in Protein-Ligand Docking." In Methods in Molecular Biology. Springer New York, 2011. http://dx.doi.org/10.1007/978-1-61779-465-0_5.

Full text
APA, Harvard, Vancouver, ISO, and other styles

Conference papers on the topic "Ligand to protein docking"

1

Kim, Chong-Min, Chung-In Won, Joonghyun Ryu, Jae-Kwan Kim, Jong Bhak, and Deok-Soo Kim. "Protein-Ligand Docking Based on ß-shape." In 2009 Sixth International Symposium on Voronoi Diagrams (ISVD). IEEE, 2009. http://dx.doi.org/10.1109/isvd.2009.27.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Atilgan, Emrah, and Jianjun Hu. "Efficient protein-ligand docking using sustainable evolutionary algorithms." In 2010 10th International Conference on Hybrid Intelligent Systems (HIS 2010). IEEE, 2010. http://dx.doi.org/10.1109/his.2010.5600082.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Pakpahan, M. T., M. Rusmerryani, K. Kawaguchi, H. Saito, and H. Nagao. "Evaluation of scoring functions for protein-ligand docking." In 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku. American Institute of Physics, 2013. http://dx.doi.org/10.1063/1.4794652.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Chun-Wei Tsai, Jui-Le Chen, and Chu-Sing Yang. "An improved LGA for protein-ligand docking prediction." In 2012 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2012. http://dx.doi.org/10.1109/cec.2012.6256513.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Atilgan, Emrah, and Jianjun Hu. "Efficient protein-ligand docking using sustainable evolutionary algorithm." In the 12th annual conference. ACM Press, 2010. http://dx.doi.org/10.1145/1830483.1830521.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Mirzaei, Hanieh, Elizabeth Villar, Scott Mottarella, et al. "Flexible refinement of protein-ligand docking on manifolds." In 2013 IEEE 52nd Annual Conference on Decision and Control (CDC). IEEE, 2013. http://dx.doi.org/10.1109/cdc.2013.6760077.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Rakshit, Pratyusha, Amit Konar, Archana Chowdhury, Eunjin Kim, and Atulya K. Nagar. "Muti-objective evolutionary approach of ligand design for protein-ligand docking problem." In 2013 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2013. http://dx.doi.org/10.1109/cec.2013.6557576.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Abramson, David, Celine Amoreira, Kim Baldridge, Laura Berstis, Chris Kondrick, and Tom Peachey. "A Flexible Grid Framework for Automatic Protein-Ligand Docking." In 2006 Second IEEE International Conference on e-Science and Grid Computing (e-Science'06). IEEE, 2006. http://dx.doi.org/10.1109/e-science.2006.261131.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Narloch, Pedro Henrique, and Marcio Dorn. "Rosetta Ligand-Protein Docking with Self-Adaptive Differential Evolution." In 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2019. http://dx.doi.org/10.1109/bibe.2019.00014.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Sapundzhi, Fatima, Krasimira Prodanova, and Meglena Lazarova. "Survey of the scoring functions for protein-ligand docking." In PROCEEDINGS OF THE 45TH INTERNATIONAL CONFERENCE ON APPLICATION OF MATHEMATICS IN ENGINEERING AND ECONOMICS (AMEE’19). AIP Publishing, 2019. http://dx.doi.org/10.1063/1.5133601.

Full text
APA, Harvard, Vancouver, ISO, and other styles

Reports on the topic "Ligand to protein docking"

1

Morris, Garrett, M., Richard K. Belew, Chris Rosin, and William Eugene Hart. Evolutionary hybrids for flexible ligand docking : (electronic notes). Office of Scientific and Technical Information (OSTI), 1999. http://dx.doi.org/10.2172/1028898.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Brummer, Tilman, and Roger J. Daly. The Role of the GAB2 Docking Protein in Human Breast Cancer. Defense Technical Information Center, 2004. http://dx.doi.org/10.21236/ada428979.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Shin, Seung-Uon. Antibody-NKG2D Ligand (Rae-1Beta) Fusion Protein for Breast Cancer Therapy. Defense Technical Information Center, 2005. http://dx.doi.org/10.21236/ada446435.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Montal, Mauricio. Channel Protein Engineering: A Novel Approach towards the Molecular Dissection Determinants in Ligand-Regulated Channels. Defense Technical Information Center, 1990. http://dx.doi.org/10.21236/ada219134.

Full text
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!