Relevant bibliographies by topics / Protein-ligand docking

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Protein-ligand docking'

Author: Grafiati
Published: 4 June 2021
Last updated: 18 February 2022

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 'Protein-ligand 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 "Protein-ligand docking"

1

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
2

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 particular, to large biological macromolecules by applying computational means to big biological data sets, and by computing biological system behavior. Computational methods used in biochemistry studies include proteomics-based bioinformatics, genome-wide mapping of protein-DNA interaction, as well as high-throughput mapping of the protein-protein interaction networks. Some of the vastly used molecular modeling and simulation techniques are Monte Carlo and Langevin (stochastic, Brownian) dynamics, statistical thermodynamics, molecular dynamics, continuum electrostatics, protein-ligand docking, protein-ligand affinity calculations, protein modeling techniques, and the protein folding process and enzyme action computer simulation. This paper presents a short review of two important methods used in the studies of biochemistry - protein-ligand docking and the prediction of protein-protein interaction networks.
APA, Harvard, Vancouver, ISO, and other styles
3

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
4

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 docking methods developed specifically for zinc proteins, GM-DockZn samples ligand conformations directly using a geometric grid around the ideal zinc-coordination positions of seven discovered coordination motifs, which were found from the survey of known zinc proteins complexed with a single ligand. Results GM-DockZn has the best performance in sampling near-native poses with correct coordination atoms and numbers within the top 50 and top 10 predictions when compared to several state-of-the-art techniques. This is true not only for a non-redundant dataset of zinc proteins but also for a homolog set of different ligand and zinc-coordination systems for the same zinc proteins. Similar superior performance of GM-DockZn for near-native-pose sampling was also observed for docking to apo-structures and cross-docking between different ligand complex structures of the same protein. The highest success rate for sampling nearest near-native poses within top 5 and top 1 was achieved by combining GM-DockZn for conformational sampling with GOLD for ranking. The proposed geometry-based sampling technique will be useful for ligand docking to other metalloproteins. Availability and implementation GM-DockZn is freely available at www.qmclab.com/ for academic users. Supplementary information Supplementary data are available at Bioinformatics online.
APA, Harvard, Vancouver, ISO, and other styles
5

Bentham Science Publisher, Bentham Science Publisher. "Scoring Functions for Protein-Ligand Docking." Current Protein & Peptide Science 7, no. 5 (2006): 407–20. http://dx.doi.org/10.2174/138920306778559395.

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

Roberts, Benjamin C., and Ricardo L. Mancera. "Ligand−Protein Docking with Water Molecules." Journal of Chemical Information and Modeling 48, no. 2 (2008): 397–408. http://dx.doi.org/10.1021/ci700285e.

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

Goto, Junichi, Ryoichi Kataoka, and Noriaki Hirayama. "Ph4Dock: Pharmacophore-Based Protein−Ligand Docking." Journal of Medicinal Chemistry 47, no. 27 (2004): 6804–11. http://dx.doi.org/10.1021/jm0493818.

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

Verdonk, Marcel L., Jason C. Cole, Michael J. Hartshorn, Christopher W. Murray, and Richard D. Taylor. "Improved protein-ligand docking using GOLD." Proteins: Structure, Function, and Bioinformatics 52, no. 4 (2003): 609–23. http://dx.doi.org/10.1002/prot.10465.

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

Pippel, Martin, Michael Scharfe, René Meier, and Wolfgang Sippl. "Einfach und frei: Protein-Ligand-Docking." Nachrichten aus der Chemie 60, no. 6 (2012): 656–57. http://dx.doi.org/10.1002/nadc.201290238.

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

Morris, Connor J., and Dennis Della Corte. "Using molecular docking and molecular dynamics to investigate protein-ligand interactions." Modern Physics Letters B 35, no. 08 (2021): 2130002. http://dx.doi.org/10.1142/s0217984921300027.

Full text
Abstract:
Molecular docking and molecular dynamics (MD) are powerful tools used to investigate protein-ligand interactions. Molecular docking programs predict the binding pose and affinity of a protein-ligand complex, while MD can be used to incorporate flexibility into docking calculations and gain further information on the kinetics and stability of the protein-ligand bond. This review covers state-of-the-art methods of using molecular docking and MD to explore protein-ligand interactions, with emphasis on application to drug discovery. We also call for further research on combining common molecular docking and MD methods.
APA, Harvard, Vancouver, ISO, and other styles
More sources

Dissertations / Theses on the topic "Protein-ligand 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 biological feasibility. The method was evaluated on a set of 310 protein-ligand complexes. The results show that with respect to docking the method with its initial parameter settings is too coarse grained. The results also show that with respect to ranking of putative active sites the method works quite well.</p>
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 that the docking procedure placed 30 to 70% of the ligand molecule correctly within 1.5A from the native structure. The discrimination potential for identification of high-affinity ligands was derived and optimised using a large set of available protein-ligand complex structures. A fast boundary-element solvation electrostatic calculation algorithm was implemented to evaluate the solvation component of the discrimination potential. An accelerated docking procedure utilising pre-calculated grid potentials was developed and tested. For 23 receptors and 63 ligands extracted from X-ray structures, the docking and discrimination protocol was capable of correct identification of the majority of native receptor-ligand couples. 51 complexes with known structures were predicted. 35 predictions were within 3A from the native structure, giving correct overall positioning of the ligand, and 26 were within 2A, reproducing a detailed picture of the receptor-ligand interaction. Docking and ligand discrimination potential evaluation was applied to screen the database of more than 150000 commercially available compounds for binding to the fibroblast growth factor receptor tyrosine kinase, the protein implicated in several pathological cell growth aberrations. As expected, a number of compounds selected by the screening protocol turned out to be known inhibitors of the tyrosine kinases. 49 putative novel ligands identified by the screening protocol were experimentally tested and five compounds have shown inhibition of phosphorylation activity of the kinase. These compounds can be used as leads for further drug development.
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 the percent of the docked complexes out of 195. On the other hand, Discovery Studio has a higher accuracy (successfully docked complexes, within 5 RMSD of the native complex structures) than AutoDock. The interaction between FADS1 and Sesamin shows a similar pattern comparing to the interaction between a homolog of FADS1 and a ligand shown in a PDB structure (PDB id 1EUE).
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 to investigate and improve molecular modelling methods aimed to estimate protein-ligand binding. In order to do so, we have utilised chemometric tools, e.g. design of experiments (DoE) and principal component analysis (PCA), in the field of molecular modelling. More specifically, molecular docking was investigated as a tool for reproduction of ligand poses in protein 3D structures and for virtual screening. Adjustable parameters in two docking software were varied using DoE and parameter settings were identified which lead to improved results. In an additional study, we explored the nature of ligand-binding cavities in proteins since they are important factors in protein-ligand interactions, especially in the prediction of the function of newly found proteins. We developed a strategy, comprising a new set of descriptors and PCA, to map proteins based on their cavity physicochemical properties. Finally, we applied our developed strategies to design a set of glycopeptides which were used to study autoimmune arthritis. A combination of docking and statistical molecular design, synthesis and biological evaluation led to new binders for two different class II MHC proteins and recognition by a panel of T-cell hybridomas. New and interesting SAR conclusions could be drawn and the results will serve as a basis for selection of peptides to include in in vivo studies.
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. Protein flexibility has been widely investigated, in terms of both local and global motions, in two diverse biological systems. On one side, Replica Exchange Molecular Dynamics has been exploited as enhanced sampling method to collect multiple conformations of Lactate Dehydrogenase A (LDHA), an emerging anticancer target. The aim of this project was the development of an Ensemble-based Virtual Screening protocol, in order to find novel potent inhibitors. On the other side, a preliminary study concerning the local flexibility of Opioid Receptors has been carried out through ALiBERO approach, an iterative method based on Elastic Network-Normal Mode Analysis and Monte Carlo sampling. Comparison of the Virtual Screening performances by using single or multiple conformations confirmed that the inclusion of protein flexibility in screening protocols has a positive effect on the probability to early recognize novel or known active compounds.
APA, Harvard, Vancouver, ISO, and other styles
More sources

Book chapters on the topic "Protein-ligand 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 "Protein-ligand 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
You might also be interested in the extended bibliographies on the topic 'Protein-ligand docking' for particular source types:
Journal articles Dissertations / Theses
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!

To the bibliography