Littérature scientifique sur le sujet « Conformational clustering »
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Articles de revues sur le sujet "Conformational clustering"
Roither, Bernhard, Chris Oostenbrink, Georg Pfeiler, Heinz Koelbl et Wolfgang Schreiner. « Pembrolizumab Induces an Unexpected Conformational Change in the CC′-loop of PD-1 ». Cancers 13, no 1 (22 décembre 2020) : 5. http://dx.doi.org/10.3390/cancers13010005.
Texte intégralConklin, D., S. Fortier, J. I. Glasgow et F. H. Allen. « Conformational analysis from crystallographic data using conceptual clustering ». Acta Crystallographica Section B Structural Science 52, no 3 (1 juin 1996) : 535–49. http://dx.doi.org/10.1107/s010876819501696x.
Texte intégralCollins, A., A. Parkin, G. Barr, W. Dong, C. J. Gilmore et C. C. Wilson. « Configurational and conformational classification of pyranose sugars ». Acta Crystallographica Section B Structural Science 64, no 1 (17 janvier 2008) : 57–65. http://dx.doi.org/10.1107/s0108768107067341.
Texte intégralHuang, Shupei, Haizhong An, Xiangyun Gao, Xiaoqing Hao et Xuan Huang. « The Multiscale Conformation Evolution of the Financial Time Series ». Mathematical Problems in Engineering 2015 (2015) : 1–9. http://dx.doi.org/10.1155/2015/563145.
Texte intégralJoshi, Arpita, Nurit Haspel et Eduardo González. « Characterizing Protein Conformational Spaces using Efficient Data Reduction and Algebraic Topology ». Journal of Human, Earth, and Future 3 (31 mai 2022) : 1–21. http://dx.doi.org/10.28991/hef-sp2022-01-01.
Texte intégralPérez, J., K. Nolsøe, M. Kessler, L. García, E. Pérez et J. L. Serrano. « Bayesian methods for the conformational classification of eight-membered rings ». Acta Crystallographica Section B Structural Science 61, no 5 (23 septembre 2005) : 585–94. http://dx.doi.org/10.1107/s0108768105023931.
Texte intégralDobrovolska, Olena, Øyvind Strømland, Ørjan Sele Handegård, Martin Jakubec, Morten L. Govasli, Åge Aleksander Skjevik, Nils Åge Frøystein, Knut Teigen et Øyvind Halskau. « Investigating the Disordered and Membrane-Active Peptide A-Cage-C Using Conformational Ensembles ». Molecules 26, no 12 (12 juin 2021) : 3607. http://dx.doi.org/10.3390/molecules26123607.
Texte intégralModi, Vivek, et Roland L. Dunbrack. « Defining a new nomenclature for the structures of active and inactive kinases ». Proceedings of the National Academy of Sciences 116, no 14 (13 mars 2019) : 6818–27. http://dx.doi.org/10.1073/pnas.1814279116.
Texte intégralHumphries, M. J. « Monoclonal antibodies as probes of integrin priming and activation ». Biochemical Society Transactions 32, no 3 (1 juin 2004) : 407–11. http://dx.doi.org/10.1042/bst0320407.
Texte intégralKessler, Mathieu, María C. Bueso et José Pérez. « Model-based conformational clustering of ring molecules ». Journal of Chemometrics 21, no 1-2 (janvier 2007) : 53–64. http://dx.doi.org/10.1002/cem.1035.
Texte intégralThèses sur le sujet "Conformational clustering"
Westerlund, Annie M. « Computational Study of Calmodulin’s Ca2+-dependent Conformational Ensembles ». Licentiate thesis, KTH, Biofysik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-234888.
Texte intégralQC 20180912
González-Alemán, Roy. « Computational fragment-based design of chemically modified oligonucleotides for selective protein inhibition : BACE1 as a case study ». Electronic Thesis or Diss., université Paris-Saclay, 2023. http://www.theses.fr/2023UPASL149.
Texte intégralFragment-based drug design (FBDD) has become an increasingly popular approach in ligand design, boasting numerous success stories within the drug discovery process. Despite some challenges relating to synthetic accessibility and ligand-design strategies, FBDD remains a promising method for addressing chemical space, molecular complexity, binding probability, and ligand efficiency. RNA therapeutics are rapidly expanding, undergoing a resurgence due to the several advantages of these molecules over traditional drugs and antibodies, including their small size, ease of synthesis, stability, and lack of immunogenicity. However, like many other drugs, off-target effects (where inhibitors designed for a specific molecule inadvertently inhibit others unintended) can hinder their usage. In this study, we introduce an in silico strategy for the fragment-based designing of a promising class of ligands: chemically modified oligonucleotides that exhibit potential selectivity for their intended targets. As a proof of concept, we employed the BACE1 enzyme, a well-established therapeutic target for Alzheimer's disease. The fragments library exploration was conducted through extensive docking simulations of mono-nucleotides using the Multiple Copy Simultaneous Search method, whose docking and screening power were rigorously assessed through a comprehensive benchmark of 121 nucleotide-protein complexes for the first time. An efficient nucleotide assembler was developed to link the best hits obtained in docking stages. Differential analysis of the best-scored oligonucleotides allowed us to find specific binding modes to BACE1 over BACE2. At a methodological level, we also propose substantial memory optimization of four widely employed clustering algorithms, which allow the identification of essential structural features for ligand-receptor binding, an integral part of any FBDD campaign
Stamatelou, Ismini Christina. « Clustering approaches for extracting structural determinants of enzyme active sites ». Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-426221.
Texte intégralAsses, Yasmine. « Conception par modélisation et criblage in silico d'inhibiteurs du récepteur c-Met ». Phd thesis, Université Henri Poincaré - Nancy I, 2011. http://tel.archives-ouvertes.fr/tel-00653609.
Texte intégralLe, Faucheur Xavier Jean Maurice. « Statistical methods for feature extraction in shape analysis and bioinformatics ». Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/33911.
Texte intégralYU, Chun-Ping, et 游竣評. « Kinetics and thermodynamics of protein-folding simulations by clustering conformational ensemble ». Thesis, 2009. http://ndltd.ncl.edu.tw/handle/18919973484035044063.
Texte intégral國立中央大學
物理研究所
97
The kinetics of the folding of the Trp-cage and protein G were studied in all-atomic molecular dynamics simulations using the AMBER 2003 force-field in implicit solvent. Replica exchange method (REM) was used to enhance sampling of folding conformational space. Folding simulations of twenty-four replicas of Trp-cage and protein G were run from extended state and native state, respectively, ranging from 276 K to 508 K. The conformational ensemble of molecular simulations was clustering by OPTICS. The results showed that the folding conformational spaces for both proteins are hierarchical. The average conformation representing centroid clustering structure for Trp-cage has a backbone root mean square deviation of 1.2 A relative to experimental structure, and 1.4 A for protein G. After regression tree analyze for mapping cluster ordering generated by OPTICS, the folding conformational space can demarcate four hierarchical regimes: unfolded state, formation of secondary structure, formation of tertiary structure, and native state. Three characterized factors for Trp-cage, Pro12-Ψ angle, Leu2-Ψ angle, and total energy, dominated folding space; and four factors for protein G: Lys4-Ψ, Thr18-Ψ, Glu42-Ψ, and Asp22-Ψ.
Huang, Fei. « Optimizing hydropathy scale to improve IDP prediction and characterizing IDPs' functions ». Thesis, 2014. http://hdl.handle.net/1805/5191.
Texte intégralIntrinsically disordered proteins (IDPs) are flexible proteins without defined 3D structures. Studies show that IDPs are abundant in nature and actively involved in numerous biological processes. Two crucial subjects in the study of IDPs lie in analyzing IDPs’ functions and identifying them. We thus carried out three projects to better understand IDPs. In the 1st project, we propose a method that separates IDPs into different function groups. We used the approach of CH-CDF plot, which is based the combined use of two predictors and subclassifies proteins into 4 groups: structured, mixed, disordered, and rare. Studies show different structural biases for each group. The mixed class has more order-promoting residues and more ordered regions than the disordered class. In addition, the disordered class is highly active in mitosis-related processes among others. Meanwhile, the mixed class is highly associated with signaling pathways, where having both ordered and disordered regions could possibly be important. The 2nd project is about identifying if an unknown protein is entirely disordered. One of the earliest predictors for this purpose, the charge-hydropathy plot (C-H plot), exploited the charge and hydropathy features of the protein. Not only is this algorithm simple yet powerful, its input parameters, charge and hydropathy, are informative and readily interpretable. We found that using different hydropathy scales significantly affects the prediction accuracy. Therefore, we sought to identify a new hydropathy scale that optimizes the prediction. This new scale achieves an accuracy of 91%, a significant improvement over the original 79%. In our 3rd project, we developed a per-residue C-H IDP predictor, in which three hydropathy scales are optimized individually. This is to account for the amino acid composition differences in three regions of a protein sequence (N, C terminus and internal). We then combined them into a single per-residue predictor that achieves an accuracy of 74% for per-residue predictions for proteins containing long IDP regions.
Chapitres de livres sur le sujet "Conformational clustering"
Bottegoni, Giovanni, Walter Rocchia et Andrea Cavalli. « Application of Conformational Clustering in Protein–Ligand Docking ». Dans Methods in Molecular Biology, 169–86. New York, NY : Springer New York, 2011. http://dx.doi.org/10.1007/978-1-61779-465-0_12.
Texte intégralAlbert, Silvana, et Gabriela Czibula. « ProteinA : An Approach for Analyzing and Visualizing Protein Conformational Transitions Using Fuzzy and Hard Clustering Techniques ». Dans Knowledge Science, Engineering and Management, 249–61. Cham : Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-29551-6_22.
Texte intégralRappuoli, R. « Introduction ». Dans Guidebook to Protein Toxins and Their Use in Cell Biology, 25–27. Oxford University PressOxford, 1997. http://dx.doi.org/10.1093/oso/9780198599555.003.0008.
Texte intégralActes de conférences sur le sujet "Conformational clustering"
Parise, L. V., B. Steiner, L. Nannizzi et D. A. Phillips. « PEPTIDES FROM FIBRINOGENAND FIBRONECTIN CHANGE THE CONFORMATIONOF PURIFIED PLATELET GLYCOPROTEIN IIb-IIIa ». Dans XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643697.
Texte intégralHaack, Fiete, Susanna Röblitz, Olga Scharkoi, Burkhard Schmidt, Marcus Weber, Theodore E. Simos, George Psihoyios et Ch Tsitouras. « Adaptive Spectral Clustering for Conformation Analysis ». Dans ICNAAM 2010 : International Conference of Numerical Analysis and Applied Mathematics 2010. AIP, 2010. http://dx.doi.org/10.1063/1.3498116.
Texte intégralGuo, Ziyi, et Brian Y. Chen. « Variational Bayesian clustering on protein cavity conformations for detecting influential amino acids ». Dans BCB '14 : ACM-BCB '14. New York, NY, USA : ACM, 2014. http://dx.doi.org/10.1145/2649387.2660837.
Texte intégralEstrada, Trlce, Roger Armen et Michela Taufer. « Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computing ». Dans the First ACM International Conference. New York, New York, USA : ACM Press, 2010. http://dx.doi.org/10.1145/1854776.1854807.
Texte intégralJukić, Marko, et Urban Bren. « Identification of small molecule binding sites using CmDock ». Dans 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.670j.
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