Academic literature on the topic 'Proteins Molecular Dynamics Computational Biophysics'
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Journal articles on the topic "Proteins Molecular Dynamics Computational Biophysics"
Liang, Zhongjie, Gennady M. Verkhivker, and Guang Hu. "Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications." Briefings in Bioinformatics 21, no. 3 (March 21, 2019): 815–35. http://dx.doi.org/10.1093/bib/bbz029.
Full textYeggoni, Daniel Pushparaju, Aparna Rachamallu, and Rajagopal Subramanyam. "A comparative binding mechanism between human serum albumin and α-1-acid glycoprotein with corilagin: biophysical and computational approach." RSC Advances 6, no. 46 (2016): 40225–37. http://dx.doi.org/10.1039/c6ra06837e.
Full textBardhan, Jaydeep P. "Gradient models in molecular biophysics: progress, challenges, opportunities." Journal of the Mechanical Behavior of Materials 22, no. 5-6 (December 1, 2013): 169–84. http://dx.doi.org/10.1515/jmbm-2013-0024.
Full textRen, Pengyu, Jaehun Chun, Dennis G. Thomas, Michael J. Schnieders, Marcelo Marucho, Jiajing Zhang, and Nathan A. Baker. "Biomolecular electrostatics and solvation: a computational perspective." Quarterly Reviews of Biophysics 45, no. 4 (November 2012): 427–91. http://dx.doi.org/10.1017/s003358351200011x.
Full textMolinski, Steven V., Zoltán Bozóky, Surtaj H. Iram, and Saumel Ahmadi. "Biophysical Approaches Facilitate Computational Drug Discovery for ATP-Binding Cassette Proteins." International Journal of Medicinal Chemistry 2017 (March 19, 2017): 1–9. http://dx.doi.org/10.1155/2017/1529402.
Full textMoffett, Alexander S., and Diwakar Shukla. "Using molecular simulation to explore the nanoscale dynamics of the plant kinome." Biochemical Journal 475, no. 5 (March 9, 2018): 905–21. http://dx.doi.org/10.1042/bcj20170299.
Full textRamos, Javier, Juan Francisco Vega, Victor Cruz, Eduardo Sanchez-Sanchez, Javier Cortes, and Javier Martinez-Salazar. "Hydrodynamic and Electrophoretic Properties of Trastuzumab/HER2 Extracellular Domain Complexes as Revealed by Experimental Techniques and Computational Simulations." International Journal of Molecular Sciences 20, no. 5 (March 1, 2019): 1076. http://dx.doi.org/10.3390/ijms20051076.
Full textOldham, William M., and Heidi E. Hamm. "Structural basis of function in heterotrimeric G proteins." Quarterly Reviews of Biophysics 39, no. 2 (May 2006): 117–66. http://dx.doi.org/10.1017/s0033583506004306.
Full textGauthier, Louis, Rémicia Di Franco, and Adrian W. R. Serohijos. "SodaPop: a forward simulation suite for the evolutionary dynamics of asexual populations on protein fitness landscapes." Bioinformatics 35, no. 20 (March 14, 2019): 4053–62. http://dx.doi.org/10.1093/bioinformatics/btz175.
Full textTang, Wai Shing, Gabriel Monteiro da Silva, Henry Kirveslahti, Erin Skeens, Bibo Feng, Timothy Sudijono, Kevin K. Yang, Sayan Mukherjee, Brenda Rubenstein, and Lorin Crawford. "A topological data analytic approach for discovering biophysical signatures in protein dynamics." PLOS Computational Biology 18, no. 5 (May 2, 2022): e1010045. http://dx.doi.org/10.1371/journal.pcbi.1010045.
Full textDissertations / Theses on the topic "Proteins Molecular Dynamics Computational Biophysics"
Rigoli, Marta. "The structure-dynamics-function relation in proteins: bridging all-atom molecular dynamics, experiments, and simplified models." Doctoral thesis, Università degli studi di Trento, 2022. https://hdl.handle.net/11572/330870.
Full textParton, Daniel L. "Pushing the boundaries : molecular dynamics simulations of complex biological membranes." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:7ab91b51-a5ae-46b4-b6dc-3f0dd3f0b477.
Full textHirst-Dunton, Thomas Alexander. "Using molecular simulations to parameterize discrete models of protein movement in the membrane." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:893568e9-696f-47e7-8495-59ecfb810459.
Full textDutta, Priyanka. "Computational Modeling of Allosteric Stimulation of Nipah Virus Host Binding Protein." Scholar Commons, 2016. http://scholarcommons.usf.edu/etd/6227.
Full textParra, Katherine Cristina. "Combination of the Computational Methods: Molecular dynamics, Homology Modeling and Docking to Design Novel Inhibitors and study Structural Changes in Target Proteins for Current Diseases." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5093.
Full textGuinto, Ferdiemar Cardenas Jr. "Investigating Secondary Structure Features of YAP1 Protein Fragments Using Molecular Dynamics (MD) and Steered Molecular Dynamics (SMD) Simulations." Scholarly Commons, 2017. https://scholarlycommons.pacific.edu/uop_etds/2973.
Full textLumb, Craig Nicholas. "Computational studies of signalling at the cell membrane." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:d5b2db00-1050-4191-8eff-3521a4885a0c.
Full textPavlovicz, Ryan Elliott. "Investigation of Protein/Ligand Interactions Relating Structural Dynamics to Function: Combined Computational and Experimental Approaches." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1397220613.
Full textCardoch, Sebastian. "Computational study of single protein sensing using nanopores." Thesis, Uppsala universitet, Materialteori, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-423441.
Full textZhou, Guangfeng. "STATISTICAL MODELS AND THEIR APPLICATIONS IN STUDYING BIOMOLECULAR CONFORMATIONAL DYNAMICS." Diss., Temple University Libraries, 2017. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/478773.
Full textPh.D.
It remains a major challenge in biophysics to understand the conformational dynamics of biomolecules. As powerful tools, molecular dynamics (MD) simulations have become increasingly important in studying the full atomic details of conformational dynamics of biomolecules. In addition, many statistical models have been developed to give insight into the big datasets from MD simulations. In this work, I first describe three statistical models used to analyze MD simulation data: Lifson-Roig Helix-Coil theory, Bayesian inference models, and Markov state models. Then I present the applications of each model in analyzing MD simulations and revealing insight into the conformational dynamics of biomolecules. These statistical models allow us to bridge microscopic and macroscopic mechanisms of biological processes and connect simulations with experiments.
Temple University--Theses
Books on the topic "Proteins Molecular Dynamics Computational Biophysics"
Sansom, M. S. P., and Philip Charles Biggin. Molecular simulations and biomembranes: From biophysics to function. Cambridge: Royal Society of Chemistry, 2010.
Find full textM, Becker Oren, ed. Computational biochemistry and biophysics. New York: M. Dekker, 2001.
Find full textDonald, Bruce R. Algorithms in structural molecular biology. Cambridge, Mass: MIT Press, 2011.
Find full textFrishman, Dmitrij. Structural bioinformatics of membrane proteins. Wien: Springer, 2010.
Find full textKostyukov, Viktor. Molecular mechanics of biopolymers. ru: INFRA-M Academic Publishing LLC., 2020. http://dx.doi.org/10.12737/1010677.
Full textFuxreiter, Monika. Computational Approaches to Protein Dynamics. Taylor & Francis Group, 2014.
Find full textFuxreiter, Monika. Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods. Taylor & Francis Group, 2014.
Find full textFuxreiter, Monika. Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods. Taylor & Francis Group, 2014.
Find full textComputational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods. Taylor & Francis Group, 2018.
Find full textComputational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods. Taylor & Francis Group, 2014.
Find full textBook chapters on the topic "Proteins Molecular Dynamics Computational Biophysics"
Eichinger, Markus, Berthold Heymann, Helmut Heller, Helmut Grubmüller, and Paul Tavan. "Conformational Dynamics Simulations of Proteins." In Computational Molecular Dynamics: Challenges, Methods, Ideas, 78–97. Berlin, Heidelberg: Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/978-3-642-58360-5_4.
Full textHelms, Volkhard, and J. Andrew McCammon. "Conformational Transitions of Proteins from Atomistic Simulations." In Computational Molecular Dynamics: Challenges, Methods, Ideas, 66–77. Berlin, Heidelberg: Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/978-3-642-58360-5_3.
Full textRodziewicz-Motowidło, Sylwia, Emilia Sikorska, and Justyna Iwaszkiewicz. "Molecular Dynamics Studies on Amyloidogenic Proteins." In Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, 445–81. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-28554-7_14.
Full textVogel, Alexander, and Daniel Huster. "Combining NMR Spectroscopy and Molecular Dynamics Simulation to Investigate the Structure and Dynamics of Membrane-Associated Proteins." In Springer Series in Biophysics, 311–50. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-66601-3_14.
Full textAntosiewicz, Jan, Elzbieta Błachut-Okrasińska, Tomasz Grycuk, James M. Briggs, Stanisław T. Włodek, Bogdan Lesyng, and J. Andrew McCammon. "Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System." In Computational Molecular Dynamics: Challenges, Methods, Ideas, 176–96. Berlin, Heidelberg: Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/978-3-642-58360-5_10.
Full textZhang, Jiapu. "A Novel Canonical Dual Global Optimization Computational Approach." In Molecular Structures and Structural Dynamics of Prion Proteins and Prions, 219–62. Dordrecht: Springer Netherlands, 2015. http://dx.doi.org/10.1007/978-94-017-7318-8_13.
Full textBarth, Marie, and Carla Schmidt. "Quantitative Cross-Linking of Proteins and Protein." In Methods in Molecular Biology, 385–400. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1024-4_26.
Full textDelemotte, Lucie. "Chapter 7. Bridging the Gap Between Atomistic Molecular Dynamics Simulations and Wet-lab Experimental Techniques: Applications to Membrane Proteins." In Theoretical and Computational Chemistry Series, 247–86. Cambridge: Royal Society of Chemistry, 2020. http://dx.doi.org/10.1039/9781788015882-00247.
Full textSljoka, Adnan. "Structural and Functional Analysis of Proteins Using Rigidity Theory." In Sublinear Computation Paradigm, 337–67. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-4095-7_14.
Full textKoch, Christof. "Diffusion, Buffering, and Binding." In Biophysics of Computation. Oxford University Press, 1998. http://dx.doi.org/10.1093/oso/9780195104912.003.0017.
Full textConference papers on the topic "Proteins Molecular Dynamics Computational Biophysics"
Stacklies, Wolfram, Frauke Gräter, Dong-Qing Wei, and Xi-Jun Wang. "Force Distribution in Proteins from Molecular Dynamics Simulations." In THEORY AND APPLICATIONS OF COMPUTATIONAL CHEMISTRY—2008. AIP, 2009. http://dx.doi.org/10.1063/1.3108379.
Full textTakasu, Masako, Hiromu Sugiyama, Yosuke Hirata, Hironao Yamada, Takeshi Miyakawa, and Ryota Morikawa. "Molecular dynamics simulation of coarse grained models of gel and proteins." In INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2015 (ICCMSE 2015). AIP Publishing LLC, 2015. http://dx.doi.org/10.1063/1.4938848.
Full textKitao, Akio, Ryuhei Harada, Yasutaka Nishihara, and Duy Phuoc Tran. "Parallel cascade selection molecular dynamics for efficient conformational sampling and free energy calculation of proteins." In INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2016 (ICCMSE 2016). Author(s), 2016. http://dx.doi.org/10.1063/1.4968639.
Full textIshioka, T., H. Yamada, T. Miyakawa, R. Morikawa, S. Akanuma, A. Yamagishi, and M. Takasu. "Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation." In INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2016 (ICCMSE 2016). Author(s), 2016. http://dx.doi.org/10.1063/1.4968649.
Full textHarada, Ryuhei, Yasutaka Nishihara, Nobuhiko Wakai, and Akio Kitao. "Conformational transition pathway and free energy analyses of proteins by parallel cascade selection molecular dynamics (PaCS-MD)." In INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2014 (ICCMSE 2014). AIP Publishing LLC, 2014. http://dx.doi.org/10.1063/1.4897682.
Full textJewel, Yead, Prashanta Dutta, and Jin Liu. "Coarse-Grained Molecular Dynamics Simulations of Sugar Transport Across Lactose Permease." In ASME 2015 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/imece2015-52337.
Full textHonarmandi, Peyman, Philip Bransford, and Roger D. Kamm. "Mechanical Properties of α-Helices Estimated Using Molecular Dynamics and Finite Element Simulations." In ASME 2008 International Mechanical Engineering Congress and Exposition. ASMEDC, 2008. http://dx.doi.org/10.1115/imece2008-69058.
Full textCortés, Juan, and Ibrahim Al-Bluwi. "A Robotics Approach to Enhance Conformational Sampling of Proteins." In ASME 2012 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/detc2012-70105.
Full textEzzEldin, Hussein M., and Santiago D. Solares. "Calculation of Isothermal Intrinsic Compressibility and Compression of GvpA Protein in Halobacterium sp. NRC-1 Using Molecular Modeling and Dynamics." In ASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2009. http://dx.doi.org/10.1115/detc2009-86265.
Full textKhan, Imad M., and Kurt S. Anderson. "A Robust Framework for Adaptive Multiscale Modeling of Biopolymers Using Highly Parallelizable Methods." In ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/nemb2013-93099.
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