Journal articles on the topic 'Proteins Molecular Dynamics Computational Biophysics'
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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 textArtali, Roberto, Antonio Del Pra, Elisabetta Foresti, Isidoro Giorgio Lesci, Norberto Roveri, and Piera Sabatino. "Adsorption of human serum albumin on the chrysotile surface: a molecular dynamics and spectroscopic investigation." Journal of The Royal Society Interface 5, no. 20 (July 11, 2007): 273–83. http://dx.doi.org/10.1098/rsif.2007.1137.
Full textMiermans, Christiaan A., and Chase P. Broedersz. "Bacterial chromosome organization by collective dynamics of SMC condensins." Journal of The Royal Society Interface 15, no. 147 (October 2018): 20180495. http://dx.doi.org/10.1098/rsif.2018.0495.
Full textSoundarrajan, Dharsan K., Francisco J. Huizar, Ramezan Paravitorghabeh, Trent Robinett, and Jeremiah J. Zartman. "From spikes to intercellular waves: Tuning intercellular calcium signaling dynamics modulates organ size control." PLOS Computational Biology 17, no. 11 (November 1, 2021): e1009543. http://dx.doi.org/10.1371/journal.pcbi.1009543.
Full textRóg, Tomasz, Mykhailo Girych, and Alex Bunker. "Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design." Pharmaceuticals 14, no. 10 (October 19, 2021): 1062. http://dx.doi.org/10.3390/ph14101062.
Full textGubieda, Alicia G., John R. Packer, Iolo Squires, Jack Martin, and Josana Rodriguez. "Going with the flow: insights from Caenorhabditis elegans zygote polarization." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1809 (August 24, 2020): 20190555. http://dx.doi.org/10.1098/rstb.2019.0555.
Full textLi, Haiyan, Zanxia Cao, Guodong Hu, Liling Zhao, Chunling Wang, and Jihua Wang. "Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations." Technology and Health Care 29 (March 25, 2021): 103–14. http://dx.doi.org/10.3233/thc-218011.
Full textVerkhivker, Gennady. "Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering." International Journal of Molecular Sciences 23, no. 6 (March 8, 2022): 2928. http://dx.doi.org/10.3390/ijms23062928.
Full textOse, Nicholas J., Brandon M. Butler, Avishek Kumar, I. Can Kazan, Maxwell Sanderford, Sudhir Kumar, and S. Banu Ozkan. "Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants." PLOS Computational Biology 18, no. 4 (April 7, 2022): e1010006. http://dx.doi.org/10.1371/journal.pcbi.1010006.
Full textHossain, Sheikh I., Neha S. Gandhi, Zak E. Hughes, and Suvash C. Saha. "Computational Modelling of the Interaction of Gold Nanoparticle with Lung Surfactant Monolayer." MRS Advances 4, no. 20 (2019): 1177–85. http://dx.doi.org/10.1557/adv.2019.93.
Full textKuwahara, Hiroyuki, and Russell Schwartz. "Stochastic steady state gain in a gene expression process with mRNA degradation control." Journal of The Royal Society Interface 9, no. 72 (January 11, 2012): 1589–98. http://dx.doi.org/10.1098/rsif.2011.0757.
Full textLu, Wei, Carlos Bueno, Nicholas P. Schafer, Joshua Moller, Shikai Jin, Xun Chen, Mingchen Chen, et al. "OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations." PLOS Computational Biology 17, no. 2 (February 12, 2021): e1008308. http://dx.doi.org/10.1371/journal.pcbi.1008308.
Full textWan, Shunzhou, Agastya P. Bhati, Stefan J. Zasada, and Peter V. Coveney. "Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction." Interface Focus 10, no. 6 (October 16, 2020): 20200007. http://dx.doi.org/10.1098/rsfs.2020.0007.
Full textPaulino, Joana, Myunggi Yi, Ivan Hung, Zhehong Gan, Xiaoling Wang, Eduard Y. Chekmenev, Huan-Xiang Zhou, and Timothy A. Cross. "Functional stability of water wire–carbonyl interactions in an ion channel." Proceedings of the National Academy of Sciences 117, no. 22 (May 15, 2020): 11908–15. http://dx.doi.org/10.1073/pnas.2001083117.
Full textWesterlund, Annie M., Akshay Sridhar, Leo Dahl, Alma Andersson, Anna-Yaroslava Bodnar, and Lucie Delemotte. "Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin." PLOS Computational Biology 18, no. 10 (October 7, 2022): e1010583. http://dx.doi.org/10.1371/journal.pcbi.1010583.
Full textWu, Yinghao, Kalyani Dhusia, and Zhaoqian Su. "Mechanistic dissection of spatial organization in NF-κB signaling pathways by hybrid simulations." Integrative Biology 13, no. 5 (April 24, 2021): 109–20. http://dx.doi.org/10.1093/intbio/zyab006.
Full textHeerwig, Andreas, Alfred Kick, Paul Sommerfeld, Sophia Eimermacher, Frederick Hartung, Markus Laube, Dietmar Fischer, et al. "The Impact of Nε-Acryloyllysine Piperazides on the Conformational Dynamics of Transglutaminase 2." International Journal of Molecular Sciences 24, no. 2 (January 13, 2023): 1650. http://dx.doi.org/10.3390/ijms24021650.
Full textSilva, Andriele, and Shaneen Singh. "Abstract 5029: A computational analysis of NEK10 and its novel protein-protein interaction with HspB1." Cancer Research 82, no. 12_Supplement (June 15, 2022): 5029. http://dx.doi.org/10.1158/1538-7445.am2022-5029.
Full textS., Udhaya Kumar, Srivarshini Sankar, Salma Younes, Thirumal Kumar D., Muneera Naseer Ahmad, Sarah Samer Okashah, Balu Kamaraj, Abeer Mohammed Al-Subaie, George Priya Doss C., and Hatem Zayed. "Deciphering the Role of Filamin B Calponin-Homology Domain in Causing the Larsen Syndrome, Boomerang Dysplasia, and Atelosteogenesis Type I Spectrum Disorders via a Computational Approach." Molecules 25, no. 23 (November 26, 2020): 5543. http://dx.doi.org/10.3390/molecules25235543.
Full textSchaaf, Gabriel, Marek Dynowski, Carl J. Mousley, Sweety D. Shah, Peihua Yuan, Eva M. Winklbauer, Marília K. F. de Campos, et al. "Resurrection of a functional phosphatidylinositol transfer protein from a pseudo-Sec14 scaffold by directed evolution." Molecular Biology of the Cell 22, no. 6 (March 15, 2011): 892–905. http://dx.doi.org/10.1091/mbc.e10-11-0903.
Full textElk, Jackson Chief, J. B. Alexander Ross, and Stephen R. Sprang. "Molecular Dynamics Investigation on Conformational Dynamics of G Proteins." Biophysical Journal 100, no. 3 (February 2011): 533a. http://dx.doi.org/10.1016/j.bpj.2010.12.3109.
Full textVaidehi, Nagarajan, Gouthaman Balaraman, In-Hee Park, Jeff Wagner, and Abhinandan Jain. "Heirarchical Constrained Molecular Dynamics Simulations for Proteins." Biophysical Journal 100, no. 3 (February 2011): 533a. http://dx.doi.org/10.1016/j.bpj.2010.12.3113.
Full textDobson, Christopher M. "Biophysical Techniques in Structural Biology." Annual Review of Biochemistry 88, no. 1 (June 20, 2019): 25–33. http://dx.doi.org/10.1146/annurev-biochem-013118-111947.
Full textHaddad, Yazan, Vojtech Adam, and Zbynek Heger. "Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins." Biophysical Journal 116, no. 11 (June 2019): 2062–72. http://dx.doi.org/10.1016/j.bpj.2019.04.017.
Full textSeshan, Shiv S. "The rigidization of water dynamics around proteins: A molecular dynamics study." Biophysical Journal 122, no. 3 (February 2023): 138a. http://dx.doi.org/10.1016/j.bpj.2022.11.909.
Full textStacklies, Wolfram, and Frauke Graeter. "Force Propagation in Proteins From Molecular Dynamics Simulations." Biophysical Journal 96, no. 3 (February 2009): 589a. http://dx.doi.org/10.1016/j.bpj.2008.12.3087.
Full textToofanny, Rudesh D., Aitziber L. Cortajarena, Lynne Regan, and Valerie Daggett. "Molecular Dynamics Simulations of Consensus Tetratricopeptide Repeat Proteins." Biophysical Journal 98, no. 3 (January 2010): 636a—637a. http://dx.doi.org/10.1016/j.bpj.2009.12.3486.
Full textTruelsen, Sigurd F. "Accelerated Molecular Dynamics Simulations of Phosphate Binding Proteins." Biophysical Journal 110, no. 3 (February 2016): 540a. http://dx.doi.org/10.1016/j.bpj.2015.11.2893.
Full textKandel, Saugat, Adrien B. Larsen, Abhinandan Jain, and Nagarajan Vaidehi. "Gneimosim: Multiscale Internal Coordinates Molecular Dynamics for Proteins." Biophysical Journal 110, no. 3 (February 2016): 641a. http://dx.doi.org/10.1016/j.bpj.2015.11.3429.
Full textHaas-Neill, Liam I., and Sarah Rauscher. "Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins." Biophysical Journal 116, no. 3 (February 2019): 432a—433a. http://dx.doi.org/10.1016/j.bpj.2018.11.2329.
Full textSridhar Dwadasi, Balarama, Hristina R. Zhekova, Sergei Y. Noskov, Dennis R. Salahub, and Peter D. Tieleman. "Constant pH molecular dynamics simulations of membrane proteins." Biophysical Journal 122, no. 3 (February 2023): 424a. http://dx.doi.org/10.1016/j.bpj.2022.11.2297.
Full textBelato, Helen B., Carmelissa Norbrun, Jinping Luo, Chinmai Pindi, Souvik Sinha, Alexandra M. D’Ordine, Gerwald Jogl, Giulia Palermo, and George P. Lisi. "Disruption of electrostatic contacts in the HNH nuclease from a thermophilic Cas9 rewires allosteric motions and enhances high-temperature DNA cleavage." Journal of Chemical Physics 157, no. 22 (December 14, 2022): 225103. http://dx.doi.org/10.1063/5.0128815.
Full textHuang, Jing. "Computational dissection of the structure-dynamics-function relationship of human solute carrier proteins." Biophysical Journal 122, no. 3 (February 2023): 507a. http://dx.doi.org/10.1016/j.bpj.2022.11.2700.
Full textDurrieu, Marie-Pierre, Richard Lavery, and Marc Baaden. "Interactions between Neuronal Fusion Proteins Explored by Molecular Dynamics." Biophysical Journal 94, no. 9 (May 2008): 3436–46. http://dx.doi.org/10.1529/biophysj.107.123117.
Full textFogolari, Federico, Alessandro Brigo, and Henriette Molinari. "Protocol for MM/PBSA Molecular Dynamics Simulations of Proteins." Biophysical Journal 85, no. 1 (July 2003): 159–66. http://dx.doi.org/10.1016/s0006-3495(03)74462-2.
Full textChilders, Matthew Carter, and Valerie Daggett. "Insights from molecular dynamics simulations for computational protein design." Molecular Systems Design & Engineering 2, no. 1 (2017): 9–33. http://dx.doi.org/10.1039/c6me00083e.
Full textDutta, Mandira, and Gregory A. Voth. "Computational studies of the dynamics of SARS-CoV-2 spike, membrane, and nucleocapsid proteins." Biophysical Journal 121, no. 3 (February 2022): 455a. http://dx.doi.org/10.1016/j.bpj.2021.11.482.
Full textBock, Lars, Brian Hutchings, Helmut Grubmüller, and Dixon J. Woodbury. "Chemomechanical Regulation of Snare Proteins Studied with Molecular Dynamics Simulations." Biophysical Journal 98, no. 3 (January 2010): 677a. http://dx.doi.org/10.1016/j.bpj.2009.12.3723.
Full textBock, Lars V., Brian Hutchings, Helmut Grubmüller, and Dixon J. Woodbury. "Chemomechanical Regulation of SNARE Proteins Studied with Molecular Dynamics Simulations." Biophysical Journal 99, no. 4 (August 2010): 1221–30. http://dx.doi.org/10.1016/j.bpj.2010.06.019.
Full textChen, Wei, Jason A. Wallace, Zhi Yue, and Jana K. Shen. "Application of Explicit-Solvent Constant ph Molecular Dynamics to Proteins." Biophysical Journal 104, no. 2 (January 2013): 508a. http://dx.doi.org/10.1016/j.bpj.2012.11.2803.
Full textHawkins, Russell, and Daniel Cox. "Elastic Moduli of Fibrous Proteins from Equilibrium Molecular Dynamics Simulation." Biophysical Journal 114, no. 3 (February 2018): 676a. http://dx.doi.org/10.1016/j.bpj.2017.11.3647.
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