Journal articles on the topic 'Protein loop modelling'
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Michalsky, E., A. Goede, and R. Preissner. "Loops In Proteins (LIP)--a comprehensive loop database for homology modelling." Protein Engineering Design and Selection 16, no. 12 (December 1, 2003): 979–85. http://dx.doi.org/10.1093/protein/gzg119.
Full textThanki, N., J. P. Zeelen, M. Mathieu, R. Jaenicke, R. A. Abagyan, R. K. Wierenga, and W. Schliebs. "Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop." Protein Engineering Design and Selection 10, no. 2 (February 1, 1997): 159–67. http://dx.doi.org/10.1093/protein/10.2.159.
Full textMacDonald, James T., Lawrence A. Kelley, and Paul S. Freemont. "Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling." PLoS ONE 8, no. 6 (June 18, 2013): e65770. http://dx.doi.org/10.1371/journal.pone.0065770.
Full textSowdhamini, R., C. Ramakrishnan, and P. Balaram. "Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and edothelin I." "Protein Engineering, Design and Selection" 6, no. 8 (1993): 873–82. http://dx.doi.org/10.1093/protein/6.8.873.
Full textTata, Rolland B., Ali F. Alsulami, Olivier Sheik Amamuddy, Tom L. Blundell, and Özlem Tastan Bishop. "Slipknot or Crystallographic Error: A Computational Analysis of the Plasmodium falciparum DHFR Structural Folds." International Journal of Molecular Sciences 23, no. 3 (January 28, 2022): 1514. http://dx.doi.org/10.3390/ijms23031514.
Full textStuder, Gabriel, Gerardo Tauriello, Stefan Bienert, Marco Biasini, Niklaus Johner, and Torsten Schwede. "ProMod3—A versatile homology modelling toolbox." PLOS Computational Biology 17, no. 1 (January 28, 2021): e1008667. http://dx.doi.org/10.1371/journal.pcbi.1008667.
Full textJezierski, G., and M. Pasenkiewicz-Gierula. "The effect of the Glu342Lys mutation in alpha1-antitrypsin on its structure, studied by molecular modelling methods." Acta Biochimica Polonica 48, no. 1 (March 31, 2001): 65–75. http://dx.doi.org/10.18388/abp.2001_5112.
Full textCollura, V. P., P. J. Greaney, and B. Robson. "A method for rapidly assessing and refining simple solvent treatments in molecular modelling. Example studies on the antigen-combining loop H2 from FAB fragment McPC603." "Protein Engineering, Design and Selection" 7, no. 2 (1994): 221–33. http://dx.doi.org/10.1093/protein/7.2.221.
Full textHuang, Qi, Monika Tokmina-Lukaszewska, Lewis E. Johnson, Hayden Kallas, Bojana Ginovska, John W. Peters, Lance C. Seefeldt, Brian Bothner, and Simone Raugei. "Mechanical coupling in the nitrogenase complex." PLOS Computational Biology 17, no. 3 (March 4, 2021): e1008719. http://dx.doi.org/10.1371/journal.pcbi.1008719.
Full textLedoux, Julie, Maxim Stolyarchuk, Enki Bachelier, Alain Trouvé, and Luba Tchertanov. "Human Vitamin K Epoxide Reductase as a Target of Its Redox Protein." International Journal of Molecular Sciences 23, no. 7 (March 31, 2022): 3899. http://dx.doi.org/10.3390/ijms23073899.
Full textRovina, Philipp, Markus Jaritz, Siegfried Höfinger, Christine Graf, Piroska Dévay, Andreas Billich, Thomas Baumruker, and Frédéric Bornancin. "A critical β6–β7 loop in the pleckstrin homology domain of ceramide kinase." Biochemical Journal 400, no. 2 (November 14, 2006): 255–65. http://dx.doi.org/10.1042/bj20060316.
Full textKolodny, Rachel, Leonidas Guibas, Michael Levitt, and Patrice Koehl. "Inverse Kinematics in Biology: The Protein Loop Closure Problem." International Journal of Robotics Research 24, no. 2-3 (February 2005): 151–63. http://dx.doi.org/10.1177/0278364905050352.
Full textLaurenzi, Tommaso, Luca Palazzolo, Elisa Taiana, Simona Saporiti, Omar Ben Mariem, Uliano Guerrini, Antonino Neri, and Ivano Eberini. "Molecular Modelling of NONO and SFPQ Dimerization Process and RNA Recognition Mechanism." International Journal of Molecular Sciences 23, no. 14 (July 10, 2022): 7626. http://dx.doi.org/10.3390/ijms23147626.
Full textWang, Guiyuan, and Zhuoqin Yang. "Stability and Hopf Bifurcation Analysis in a Delayed Myc/E2F/miR-17-92 Network Involving Interlinked Positive and Negative Feedback Loops." Discrete Dynamics in Nature and Society 2018 (November 11, 2018): 1–12. http://dx.doi.org/10.1155/2018/7014789.
Full textAbbass, Jad, and Jean-Christophe Nebel. "Rosetta and the Journey to Predict Proteins’ Structures, 20 Years on." Current Bioinformatics 15, no. 6 (November 11, 2020): 611–28. http://dx.doi.org/10.2174/1574893615999200504103643.
Full textMellor, Greg J., Pankaj Panwar, Andrea K. Lee, Christian Steinberg, Julie A. Hathaway, Kirsten Bartels, Susan Christian, et al. "Type 8 long QT syndrome: pathogenic variants in CACNA1C-encoded Cav1.2 cluster in STAC protein binding site." EP Europace 21, no. 11 (August 13, 2019): 1725–32. http://dx.doi.org/10.1093/europace/euz215.
Full textBernard, Samuel, Branka Čajavec, Laurent Pujo-Menjouet, Michael C. Mackey, and Hanspeter Herzel. "Modelling transcriptional feedback loops: the role of Gro/TLE1 in Hes1 oscillations." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 364, no. 1842 (March 21, 2006): 1155–70. http://dx.doi.org/10.1098/rsta.2006.1761.
Full textWoolley, Michael J., Harriet A. Watkins, Bruck Taddese, Z. Gamze Karakullukcu, James Barwell, Kevin J. Smith, Debbie L. Hay, David R. Poyner, Christopher A. Reynolds, and Alex C. Conner. "The role of ECL2 in CGRP receptor activation: a combined modelling and experimental approach." Journal of The Royal Society Interface 10, no. 88 (November 6, 2013): 20130589. http://dx.doi.org/10.1098/rsif.2013.0589.
Full textMacdonald, Andrew, Sabine Mazaleyrat, Christopher McCormick, Andrew Street, Nicholas J. Burgoyne, Richard M. Jackson, Virginie Cazeaux, Holly Shelton, Kalle Saksela, and Mark Harris. "Further studies on hepatitis C virus NS5A–SH3 domain interactions: identification of residues critical for binding and implications for viral RNA replication and modulation of cell signalling." Journal of General Virology 86, no. 4 (April 1, 2005): 1035–44. http://dx.doi.org/10.1099/vir.0.80734-0.
Full textSardiñas, Gretel, Daniel Yero, Yanet Climent, Evelin Caballero, Karem Cobas, and Olivia Niebla. "Neisseria meningitidis antigen NMB0088: sequence variability, protein topology and vaccine potential." Journal of Medical Microbiology 58, no. 2 (February 1, 2009): 196–208. http://dx.doi.org/10.1099/jmm.0.004820-0.
Full textSOH, Yunjo, Byoung J. SONG, Jiingjau JENG, and Abraham T. KALLARAKAL. "Critical role of Arg433 in rat transketolase activity as probed by site-directed mutagenesis." Biochemical Journal 333, no. 2 (July 15, 1998): 367–72. http://dx.doi.org/10.1042/bj3330367.
Full textJeong, Dae Gwin, Chun Hua Wei, Bonsu Ku, Tae Jin Jeon, Pham Ngoc Chien, Jae Kwan Kim, So Ya Park, et al. "The family-wide structure and function of human dual-specificity protein phosphatases." Acta Crystallographica Section D Biological Crystallography 70, no. 2 (January 29, 2014): 421–35. http://dx.doi.org/10.1107/s1399004713029866.
Full textJiang, Leanne, and Shyuan T. Ngo. "Altered TDP-43 Structure and Function: Key Insights into Aberrant RNA, Mitochondrial, and Cellular and Systemic Metabolism in Amyotrophic Lateral Sclerosis." Metabolites 12, no. 8 (July 29, 2022): 709. http://dx.doi.org/10.3390/metabo12080709.
Full textSajid, Moon, Shane R. Stone, and Parwinder Kaur. "Phylogenetic Analysis and Protein Modelling of Isoflavonoid Synthase Highlights Key Catalytic Sites towards Realising New Bioengineering Endeavours." Bioengineering 9, no. 11 (October 24, 2022): 609. http://dx.doi.org/10.3390/bioengineering9110609.
Full textMishra, Manasi, Vigyasa Singh, Meenakshi B. Tellis, Rakesh S. Joshi, and Shailja Singh. "Repurposing the McoTI-II Rigid Molecular Scaffold in to Inhibitor of ‘Papain Superfamily’ Cysteine Proteases." Pharmaceuticals 14, no. 1 (December 23, 2020): 7. http://dx.doi.org/10.3390/ph14010007.
Full textSajnaga, Ewa, Konrad Kubiński, and Ryszard Szyszka. "Catalytic activity of mutants of yeast protein kinase CK2alpha." Acta Biochimica Polonica 55, no. 4 (November 17, 2008): 767–76. http://dx.doi.org/10.18388/abp.2008_3039.
Full textRAJAMOHAN, Govindan, Monika DAHIYA, Shekhar C. MANDE, and Kanak L. DIKSHIT. "Function of the 90-loop (Thr90–Glu100) region of staphylokinase in plasminogen activation probed through site-directed mutagenesis and loop deletion." Biochemical Journal 365, no. 2 (July 15, 2002): 379–89. http://dx.doi.org/10.1042/bj20011647.
Full textChowdhury, Sourav, Dwipanjan Sanyal, Sagnik Sen, Vladimir N. Uversky, Ujjwal Maulik, and Krishnananda Chattopadhyay. "Evolutionary Analyses of Sequence and Structure Space Unravel the Structural Facets of SOD1." Biomolecules 9, no. 12 (December 4, 2019): 826. http://dx.doi.org/10.3390/biom9120826.
Full textGeorge, Biju, Rajrani Ruhel, Mohit Mazumder, Veerendra Kumar Sharma, Swatantra Kumar Jain, Samudrala Gourinath, and Supriya Chakraborty. "Mutational analysis of the helicase domain of a replication initiator protein reveals critical roles of Lys 272 of the B′ motif and Lys 289 of the β-hairpin loop in geminivirus replication." Journal of General Virology 95, no. 7 (July 1, 2014): 1591–602. http://dx.doi.org/10.1099/vir.0.064923-0.
Full textYan, Fang, Li Liu, and Qingyun Wang. "Combinatorial dynamics of protein synthesis time delay and negative feedback loop in NF-κB signalling pathway." IET Systems Biology 14, no. 5 (October 1, 2020): 284–91. http://dx.doi.org/10.1049/iet-syb.2020.0034.
Full textModahl, Cassandra M., Mrinalini, Seth Frietze, and Stephen P. Mackessy. "Adaptive evolution of distinct prey-specific toxin genes in rear-fanged snake venom." Proceedings of the Royal Society B: Biological Sciences 285, no. 1884 (August 2018): 20181003. http://dx.doi.org/10.1098/rspb.2018.1003.
Full textChen, Ting, Haiying Wu, Chenxi Zhang, Jiarong Feng, Linqi Chen, Rongrong Xie, Fengyun Wang, et al. "Clinical, Genetics, and Bioinformatic Characterization of Mutations Affecting an Essential Region of PLS3 in Patients with BMND18." International Journal of Endocrinology 2018 (October 14, 2018): 1–9. http://dx.doi.org/10.1155/2018/8953217.
Full textKoide, Hiroki, Noriyuki Kodera, Shveta Bisht, Shoji Takada, and Tsuyoshi Terakawa. "Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy." PLOS Computational Biology 17, no. 7 (July 30, 2021): e1009265. http://dx.doi.org/10.1371/journal.pcbi.1009265.
Full textEhresmann, Chantal, Claude Philippe, E. Westhof, Bernard Ehresmann, Lionel Bénard, and Claude Portier. "A pseudoknot is required for efficient translational initiation and regulation of the Escherichia coli rpsO gene coding for ribosomal protein S15." Biochemistry and Cell Biology 73, no. 11-12 (December 1, 1995): 1131–40. http://dx.doi.org/10.1139/o95-122.
Full textGhomlaghi, Milad, Guang Yang, Sungyoung Shin, David E. James, and Lan K. Nguyen. "Dynamic modelling of the PI3K/MTOR signalling network uncovers biphasic dependence of mTORC1 activity on the mTORC2 subunit SIN1." PLOS Computational Biology 17, no. 9 (September 16, 2021): e1008513. http://dx.doi.org/10.1371/journal.pcbi.1008513.
Full textBell, S., J. R. Matthews, E. Jaffray, and R. T. Hay. "I(kappa)B(gamma) inhibits DNA binding of NF-kappaB p50 homodimers by interacting with residues that contact DNA." Molecular and Cellular Biology 16, no. 11 (November 1996): 6477–85. http://dx.doi.org/10.1128/mcb.16.11.6477.
Full textModi, Saurabh, Supravat Dey, and Abhyudai Singh. "Noise suppression in stochastic genetic circuits using PID controllers." PLOS Computational Biology 17, no. 7 (July 28, 2021): e1009249. http://dx.doi.org/10.1371/journal.pcbi.1009249.
Full textQaid, Talal S., Hussein Mazaar, Mohammed S. Alqahtani, Abeer A. Raweh, and Wafaa Alakwaa. "Deep sequence modelling for predicting COVID-19 mRNA vaccine degradation." PeerJ Computer Science 7 (June 22, 2021): e597. http://dx.doi.org/10.7717/peerj-cs.597.
Full textAbella, Jayvee, Dinler Antunes, Cecilia Clementi, and Lydia Kavraki. "APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations." Molecules 24, no. 5 (March 2, 2019): 881. http://dx.doi.org/10.3390/molecules24050881.
Full textLi, Xiao-Quan, Li-Wen Qiu, Yue Chen, Kun Wen, Jian-Piao Cai, Jing Chen, Yu-Xian Pan, et al. "Dengue virus envelope domain III immunization elicits predominantly cross-reactive, poorly neutralizing antibodies localized to the AB loop: implications for dengue vaccine design." Journal of General Virology 94, no. 10 (October 1, 2013): 2191–201. http://dx.doi.org/10.1099/vir.0.055178-0.
Full textMeh, Primož, Miha Pavšič, Vito Turk, Antonio Baici, and Brigita Lenarčič. "Dual concentration-dependent activity of thyroglobulin type-1 domain of testican: specific inhibitor and substrate of cathepsin L." Biological Chemistry 386, no. 1 (January 1, 2005): 75–83. http://dx.doi.org/10.1515/bc.2005.010.
Full textTang, Ke, Jinfeng Zhang, and Jie Liang. "Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method." PLoS Computational Biology 10, no. 4 (April 24, 2014): e1003539. http://dx.doi.org/10.1371/journal.pcbi.1003539.
Full textZhan, Jingyu, Angela R. Harrison, Stephanie Portelli, Thanh Binh Nguyen, Isshu Kojima, Siqiong Zheng, Fei Yan, et al. "Definition of the immune evasion-replication interface of rabies virus P protein." PLOS Pathogens 17, no. 7 (July 8, 2021): e1009729. http://dx.doi.org/10.1371/journal.ppat.1009729.
Full textShelden, Megan C., Susan M. Howitt, Brent N. Kaiser, and Stephen D. Tyerman. "Identification and functional characterisation of aquaporins in the grapevine, Vitis vinifera." Functional Plant Biology 36, no. 12 (2009): 1065. http://dx.doi.org/10.1071/fp09117.
Full textGorgoni, Barbara, Yun-Bo Zhao, J. Krishnan, and Ian Stansfield. "Destabilization of Eukaryote mRNAs by 5′ Proximal Stop Codons Can Occur Independently of the Nonsense-Mediated mRNA Decay Pathway." Cells 8, no. 8 (July 31, 2019): 800. http://dx.doi.org/10.3390/cells8080800.
Full textVohra, Shabana, Bruck Taddese, Alex C. Conner, David R. Poyner, Debbie L. Hay, James Barwell, Philip J. Reeves, Graham J. G. Upton, and Christopher A. Reynolds. "Similarity between class A and class B G-protein-coupled receptors exemplified through calcitonin gene-related peptide receptor modelling and mutagenesis studies." Journal of The Royal Society Interface 10, no. 79 (February 6, 2013): 20120846. http://dx.doi.org/10.1098/rsif.2012.0846.
Full textJeyakanthan, Jeyaraman, Shankar Prasad Kanaujia, Yuya Nishida, Noriko Nakagawa, Surendran Praveen, Akeo Shinkai, Seiki Kuramitsu, Shigeyuki Yokoyama, and Kanagaraj Sekar. "Free and ATP-bound structures of Ap4A hydrolase fromAquifex aeolicusV5." Acta Crystallographica Section D Biological Crystallography 66, no. 2 (January 22, 2010): 116–24. http://dx.doi.org/10.1107/s0907444909047064.
Full textRao, Francesco V., Alexander W. Schüttelkopf, Helge C. Dorfmueller, Andrew T. Ferenbach, Iva Navratilova, and Daan M. F. van Aalten. "Structure of a bacterial putative acetyltransferase defines the fold of the human O -GlcNAcase C-terminal domain." Open Biology 3, no. 10 (October 2013): 130021. http://dx.doi.org/10.1098/rsob.130021.
Full textRodrigues-Amorim, Daniela, Marta Iglesias-Martínez-Almeida, Tania Rivera-Baltanás, Patricia Fernández-Palleiro, Luis Freiría-Martínez, Cynthia Rodríguez-Jamardo, María Comís-Tuche, et al. "The Role of the Second Extracellular Loop of Norepinephrine Transporter, Neurotrophin-3 and Tropomyosin Receptor Kinase C in T Cells: A Peripheral Biomarker in the Etiology of Schizophrenia." International Journal of Molecular Sciences 22, no. 16 (August 7, 2021): 8499. http://dx.doi.org/10.3390/ijms22168499.
Full textDas, Chinmaya Kumar, Umasankar Nayak, Preetinanda Pati, Mihir Ranjan Mohanty, Sujata Das, Parshuram Sial, Bhagban Kabat, and S. C. Swain. "Deciphering the Molecular Architecture of a Candidate R-gene (BjuWRR1) Product Mediating White Rust Resistance in Brassica juncea." International Journal of Bio-resource and Stress Management 12, no. 5 (August 31, 2021): 393–401. http://dx.doi.org/10.23910/1.2021.2205a.
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