Статті в журналах з теми "Protein Structure Models"
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Mucsi, Z., Z. Gaspari, G. Orosz, and A. Perczel. "Structure-oriented rational design of chymotrypsin inhibitor models." Protein Engineering Design and Selection 16, no. 9 (September 1, 2003): 673–81. http://dx.doi.org/10.1093/protein/gzg090.
Повний текст джерелаKim, HyungRae. "Residue Environment Score for Selecting Protein Structure Models and Protein-Protein Docking Models." Biophysical Journal 110, no. 3 (February 2016): 346a. http://dx.doi.org/10.1016/j.bpj.2015.11.1862.
Повний текст джерелаKoliński, A., and J. Skolnick. "High coordination lattice models of protein structure, dynamics and thermodynamics." Acta Biochimica Polonica 44, no. 3 (September 30, 1997): 389–422. http://dx.doi.org/10.18388/abp.1997_4393.
Повний текст джерелаYang, Yifeng David, Preston Spratt, Hao Chen, Changsoon Park, and Daisuke Kihara. "Sub-AQUA: real-value quality assessment of protein structure models." Protein Engineering, Design and Selection 23, no. 8 (June 4, 2010): 617–32. http://dx.doi.org/10.1093/protein/gzq030.
Повний текст джерелаKihara, Daisuke, Hao Chen, and Yifeng Yang. "Quality Assessment of Protein Structure Models." Current Protein & Peptide Science 10, no. 3 (June 1, 2009): 216–28. http://dx.doi.org/10.2174/138920309788452173.
Повний текст джерелаHirsch, M., and M. Habeck. "Mixture models for protein structure ensembles." Bioinformatics 24, no. 19 (July 28, 2008): 2184–92. http://dx.doi.org/10.1093/bioinformatics/btn396.
Повний текст джерелаGhosh, Soma, and Saraswathi Vishveshwara. "Ranking the quality of protein structure models using sidechain based network properties." F1000Research 3 (January 21, 2014): 17. http://dx.doi.org/10.12688/f1000research.3-17.v1.
Повний текст джерелаDomingues, F. S., J. Rahnenfuhrer, and T. Lengauer. "Automated clustering of ensembles of alternative models in protein structure databases." Protein Engineering Design and Selection 17, no. 6 (August 3, 2004): 537–43. http://dx.doi.org/10.1093/protein/gzh063.
Повний текст джерелаShatabda, Swakkhar, M. A. Hakim Newton, Mahmood A. Rashid, Duc Nghia Pham, and Abdul Sattar. "How Good Are Simplified Models for Protein Structure Prediction?" Advances in Bioinformatics 2014 (April 29, 2014): 1–9. http://dx.doi.org/10.1155/2014/867179.
Повний текст джерелаBienkowska, J., Hongxian He, and T. F. Smith. "Automatic pattern embedding in protein structure models." IEEE Intelligent Systems 16, no. 6 (November 2001): 21–25. http://dx.doi.org/10.1109/5254.972074.
Повний текст джерелаJamroz, Michal, Andrzej Kolinski, and Daisuke Kihara. "Ensemble-based evaluation for protein structure models." Bioinformatics 32, no. 12 (June 15, 2016): i314—i321. http://dx.doi.org/10.1093/bioinformatics/btw262.
Повний текст джерелаKarplus, Kevin, Kimmen Sjölander, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, Liisa Holm, and Chris Sander. "Predicting protein structure using hidden Markov models." Proteins: Structure, Function, and Genetics 29, S1 (1997): 134–39. http://dx.doi.org/10.1002/(sici)1097-0134(1997)1+<134::aid-prot18>3.0.co;2-p.
Повний текст джерелаBastolla, Ugo. "Computing protein dynamics from protein structure with elastic network models." Wiley Interdisciplinary Reviews: Computational Molecular Science 4, no. 5 (April 18, 2014): 488–503. http://dx.doi.org/10.1002/wcms.1186.
Повний текст джерелаZhou, Xiaogen, Jun Hu, Chengxin Zhang, Guijun Zhang, and Yang Zhang. "Assembling multidomain protein structures through analogous global structural alignments." Proceedings of the National Academy of Sciences 116, no. 32 (July 24, 2019): 15930–38. http://dx.doi.org/10.1073/pnas.1905068116.
Повний текст джерелаFlechsig, Holger, and Yuichi Togashi. "Designed Elastic Networks: Models of Complex Protein Machinery." International Journal of Molecular Sciences 19, no. 10 (October 13, 2018): 3152. http://dx.doi.org/10.3390/ijms19103152.
Повний текст джерелаRobic, Srebrenka. "Mathematics, Thermodynamics, and Modeling to Address Ten Common Misconceptions about Protein Structure, Folding, and Stability." CBE—Life Sciences Education 9, no. 3 (September 2010): 189–95. http://dx.doi.org/10.1187/cbe.10-03-0018.
Повний текст джерелаPerez, Alberto, Zheng Yang, Ivet Bahar, Ken A. Dill, and Justin L. MacCallum. "FlexE: Using Elastic Network Models to Compare Models of Protein Structure." Journal of Chemical Theory and Computation 8, no. 10 (April 26, 2012): 3985–91. http://dx.doi.org/10.1021/ct300148f.
Повний текст джерелаvan Beusekom, Bart, Natasja Wezel, Maarten L. Hekkelman, Anastassis Perrakis, Paul Emsley, and Robbie P. Joosten. "Building and rebuilding N-glycans in protein structure models." Acta Crystallographica Section D Structural Biology 75, no. 4 (April 1, 2019): 416–25. http://dx.doi.org/10.1107/s2059798319003875.
Повний текст джерелаAzulay, Hay, Aviv Lutaty, and Nir Qvit. "How Similar Are Proteins and Origami?" Biomolecules 12, no. 5 (April 21, 2022): 622. http://dx.doi.org/10.3390/biom12050622.
Повний текст джерелаGáspári, Zoltán, and László Nyitray. "Coiled coils as possible models of protein structure evolution." BioMolecular Concepts 2, no. 3 (June 1, 2011): 199–210. http://dx.doi.org/10.1515/bmc.2011.015.
Повний текст джерелаMascarenhas, Nahren Manuel, and Shachi Gosavi. "Understanding protein domain-swapping using structure-based models of protein folding." Progress in Biophysics and Molecular Biology 128 (September 2017): 113–20. http://dx.doi.org/10.1016/j.pbiomolbio.2016.09.013.
Повний текст джерелаWang, Wenkai, Zhenling Peng, and Jianyi Yang. "Single-sequence protein structure prediction using supervised transformer protein language models." Nature Computational Science 2, no. 12 (December 19, 2022): 804–14. http://dx.doi.org/10.1038/s43588-022-00373-3.
Повний текст джерелаSasaki, J., T. Terada, S. Nakamura, and K. shimizu. "Evaluation of protein structure prediction models by computers." Seibutsu Butsuri 43, supplement (2003): S90. http://dx.doi.org/10.2142/biophys.43.s90_1.
Повний текст джерелаSanchez, R. "ModBase: A database of comparative protein structure models." Bioinformatics 15, no. 12 (December 1, 1999): 1060–61. http://dx.doi.org/10.1093/bioinformatics/15.12.1060.
Повний текст джерелаNeelamraju, Sridhar, David J. Wales, and Shachi Gosavi. "Protein energy landscape exploration with structure-based models." Current Opinion in Structural Biology 64 (October 2020): 145–51. http://dx.doi.org/10.1016/j.sbi.2020.07.003.
Повний текст джерелаMonroe, Lyman, Genki Terashi, and Daisuke Kihara. "Variability of Protein Structure Models from Electron Microscopy." Structure 25, no. 4 (April 2017): 592–602. http://dx.doi.org/10.1016/j.str.2017.02.004.
Повний текст джерелаTaylor, William R. "Decoy Models for Protein Structure Comparison Score Normalisation." Journal of Molecular Biology 357, no. 2 (March 2006): 676–99. http://dx.doi.org/10.1016/j.jmb.2005.12.084.
Повний текст джерелаKota, Pradeep, Feng Ding, Srinivas Ramachandran, and Nikolay V. Dokholyan. "Gaia: automated quality assessment of protein structure models." Bioinformatics 27, no. 16 (June 23, 2011): 2209–15. http://dx.doi.org/10.1093/bioinformatics/btr374.
Повний текст джерелаYuan, Xin, Yu Shao, and Christopher Bystroff. "Ab Initio Protein Structure Prediction Using Pathway Models." Comparative and Functional Genomics 4, no. 4 (2003): 397–401. http://dx.doi.org/10.1002/cfg.305.
Повний текст джерелаVaradi, M., M. Deshpande, S. Nair, S. Anyango, D. Bertoni, and S. Velankar. "High-accuracy protein structure models in AlphaFold DB." Acta Crystallographica Section A Foundations and Advances 78, a2 (August 23, 2022): a436. http://dx.doi.org/10.1107/s2053273322093044.
Повний текст джерелаEyre, T. A., L. Partridge, and J. M. Thornton. "Computational analysis of -helical membrane protein structure: implications for the prediction of 3D structural models." Protein Engineering Design and Selection 17, no. 8 (September 23, 2004): 613–24. http://dx.doi.org/10.1093/protein/gzh072.
Повний текст джерелаGaasterland, Teri. "Strategies for Structural Genomics Target Selection." Scientific World JOURNAL 2 (2002): 67. http://dx.doi.org/10.1100/tsw.2002.33.
Повний текст джерелаThomas, Jens, Ronan Keegan, Jaclyn Bibby, Martyn Winn, Olga Mayans, and Daniel Rigden. "Rapid molecular replacement of coiled-coil and transmembrane proteins with AMPLE." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C347. http://dx.doi.org/10.1107/s2053273314096521.
Повний текст джерелаDuong, Vy T., Elizabeth M. Diessner, Gianmarc Grazioli, Rachel W. Martin, and Carter T. Butts. "Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures." Biomolecules 11, no. 12 (November 30, 2021): 1788. http://dx.doi.org/10.3390/biom11121788.
Повний текст джерелаPerkins, Stephen J., and Alexandra Bonner. "Structure determinations of human and chimaeric antibodies by solution scattering and constrained molecular modelling." Biochemical Society Transactions 36, no. 1 (January 22, 2008): 37–42. http://dx.doi.org/10.1042/bst0360037.
Повний текст джерелаKmiecik, Sebastian, Maksim Kouza, Aleksandra Badaczewska-Dawid, Andrzej Kloczkowski, and Andrzej Kolinski. "Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models." International Journal of Molecular Sciences 19, no. 11 (November 6, 2018): 3496. http://dx.doi.org/10.3390/ijms19113496.
Повний текст джерелаAzzaz, Fodil, and Jacques Fantini. "The epigenetic dimension of protein structure." Biomolecular Concepts 13, no. 1 (January 1, 2022): 55–60. http://dx.doi.org/10.1515/bmc-2022-0006.
Повний текст джерелаChakravarty, S. "Accuracy of structure-derived properties in simple comparative models of protein structures." Nucleic Acids Research 33, no. 1 (January 7, 2005): 244–59. http://dx.doi.org/10.1093/nar/gki162.
Повний текст джерелаGuo, Yuzhi, Jiaxiang Wu, Hehuan Ma, and Junzhou Huang. "Self-Supervised Pre-training for Protein Embeddings Using Tertiary Structures." Proceedings of the AAAI Conference on Artificial Intelligence 36, no. 6 (June 28, 2022): 6801–9. http://dx.doi.org/10.1609/aaai.v36i6.20636.
Повний текст джерелаFontove, Fernando, and Gabriel Del Rio. "Residue Cluster Classes: A Unified Protein Representation for Efficient Structural and Functional Classification." Entropy 22, no. 4 (April 20, 2020): 472. http://dx.doi.org/10.3390/e22040472.
Повний текст джерелаLampros, Christos, Thomas Simos, Themis P. Exarchos, Konstantinos P. Exarchos, Costas Papaloukas, and Dimitrios I. Fotiadis. "Assessment of optimized Markov models in protein fold classification." Journal of Bioinformatics and Computational Biology 12, no. 04 (August 2014): 1450016. http://dx.doi.org/10.1142/s0219720014500164.
Повний текст джерелаMacCallum, Justin L., Alberto Perez, and Ken A. Dill. "Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference." Proceedings of the National Academy of Sciences 112, no. 22 (May 18, 2015): 6985–90. http://dx.doi.org/10.1073/pnas.1506788112.
Повний текст джерелаLin, Zeming, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Nikita Smetanin, et al. "Evolutionary-scale prediction of atomic-level protein structure with a language model." Science 379, no. 6637 (March 17, 2023): 1123–30. http://dx.doi.org/10.1126/science.ade2574.
Повний текст джерелаAubel, Margaux, Lars Eicholt, and Erich Bornberg-Bauer. "Assessing structure and disorder prediction tools for de novo emerged proteins in the age of machine learning." F1000Research 12 (March 29, 2023): 347. http://dx.doi.org/10.12688/f1000research.130443.1.
Повний текст джерелаGORIELY, ALAIN, ANDREW HAUSRATH, and SÉBASTIEN NEUKIRCH. "THE DIFFERENTIAL GEOMETRY OF PROTEINS AND ITS APPLICATIONS TO STRUCTURE DETERMINATION." Biophysical Reviews and Letters 03, no. 01n02 (April 2008): 77–101. http://dx.doi.org/10.1142/s1793048008000629.
Повний текст джерелаPrajapat, Rajneesh, Avinash Marwal, and R. K. Gaur. "Recognition of Errors in the Refinement and Validation of Three-Dimensional Structures of AC1 Proteins of Begomovirus Strains by Using ProSA-Web." Journal of Viruses 2014 (January 2, 2014): 1–6. http://dx.doi.org/10.1155/2014/752656.
Повний текст джерелаRashid, Mahmood A., M. A. Hakim Newton, Md Tamjidul Hoque, and Abdul Sattar. "Mixing Energy Models in Genetic Algorithms for On-Lattice Protein Structure Prediction." BioMed Research International 2013 (2013): 1–15. http://dx.doi.org/10.1155/2013/924137.
Повний текст джерелаAdiyaman and McGuffin. "Methods for the Refinement of Protein Structure 3D Models." International Journal of Molecular Sciences 20, no. 9 (May 9, 2019): 2301. http://dx.doi.org/10.3390/ijms20092301.
Повний текст джерелаPieper, U. "MODBASE, a database of annotated comparative protein structure models." Nucleic Acids Research 30, no. 1 (January 1, 2002): 255–59. http://dx.doi.org/10.1093/nar/30.1.255.
Повний текст джерелаSanchez, R. "MODBASE, a database of annotated comparative protein structure models." Nucleic Acids Research 28, no. 1 (January 1, 2000): 250–53. http://dx.doi.org/10.1093/nar/28.1.250.
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