Relevant bibliographies by topics / Protein-molecule interactions

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Protein-molecule interactions'

Author: Grafiati
Published: 26 October 2024
Last updated: 31 July 2025

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Journal articles on the topic "Protein-molecule interactions"

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Kuusk, Ave, Helen Boyd, Hongming Chen, and Christian Ottmann. "Small-molecule modulation of p53 protein-protein interactions." Biological Chemistry 401, no. 8 (2020): 921–31. http://dx.doi.org/10.1515/hsz-2019-0405.

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AbstractSmall-molecule modulation of protein-protein interactions (PPIs) is a very promising but also challenging area in drug discovery. The tumor suppressor protein p53 is one of the most frequently altered proteins in human cancers, making it an attractive target in oncology. 14-3-3 proteins have been shown to bind to and positively regulate p53 activity by protecting it from MDM2-dependent degradation or activating its DNA binding affinity. PPIs can be modulated by inhibiting or stabilizing specific interactions by small molecules. Whereas inhibition has been widely explored by the pharmac
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Ottmann, Christian. "Small-molecule modulation of protein–protein interactions." Drug Discovery Today: Technologies 10, no. 4 (2013): e499-e500. http://dx.doi.org/10.1016/j.ddtec.2013.08.001.

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Pollock, Julie A., Courtney L. Labrecque, Cassidy N. Hilton, et al. "Small Molecule Modulation of MEMO1 Protein-Protein Interactions." Journal of the Endocrine Society 5, Supplement_1 (2021): A1031. http://dx.doi.org/10.1210/jendso/bvab048.2110.

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Abstract MEMO1 (mediator of ErbB2-driven cell motility) is upregulated in breast tumors and has been correlated with poor prognosis in patients. As a scaffolding protein that binds to phosphorylated-tyrosine residues on receptors such as estrogen receptor and ErbB2, MEMO1 levels can influence phosphorylation cascades. Using our previously developed fluorescence polarization assay, we have identified small molecules with the ability to disrupt the interactions of MEMO1. We have performed limited structure-activity-relationship studies and computational analyses to investigate the molecular requ
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Guo, Z. "Designing Small-Molecule Switches for Protein-Protein Interactions." Science 288, no. 5473 (2000): 2042–45. http://dx.doi.org/10.1126/science.288.5473.2042.

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SAHA, MIRABEAU, and TIMOLÉON C. KOFANÉ. "NONLINEAR DYNAMICS OF LONG-RANGE PROTEIN-HELICOIDAL DNA INTERACTIONS." International Journal of Modern Physics B 26, no. 19 (2012): 1250101. http://dx.doi.org/10.1142/s0217979212501019.

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The effects of long-range interactions between peptides on the protein–DNA dynamics in the long-wave limit are studied. The investigation, done at the physiological temperature, is based on a coupled spin system of DNA molecule which includes the helicoidal geometry of DNA molecule and the Kac–Baker long-range interaction between the peptides of the protein molecule. By using the Holstein–Primakoff bosonic representation of the spin operators, we show that the original discrete equations for the protein–DNA interaction dynamics can be reduced to the nonlinear Schrödinger (NLS) equation of whic
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Nemashkalo, A., M. E. Phipps, S. P. Hennelly, and P. M. Goodwin. "Real-time, single-molecule observation of biomolecular interactions inside nanophotonic zero mode waveguides." Nanotechnology 33, no. 16 (2022): 165101. http://dx.doi.org/10.1088/1361-6528/ac467c.

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Abstract Living cells rely on numerous protein-protein, RNA-protein and DNA-protein interactions for processes such as gene expression, biomolecular assembly, protein and RNA degradation. Single-molecule microscopy and spectroscopy are ideal tools for real-time observation and quantification of nucleic acids-protein and protein-protein interactions. One of the major drawbacks of conventional single-molecule imaging methods is low throughput. Methods such as sequencing by synthesis utilizing nanofabrication and single-molecule spectroscopy have brought high throughput into the realm of single-m
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D’Abramo, C. M. "Small Molecule Inhibitors of Human Papillomavirus Protein - Protein Interactions." Open Virology Journal 5, no. 1 (2011): 80–95. http://dx.doi.org/10.2174/1874357901105010080.

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Linhares, Brian M., Jolanta Grembecka, and Tomasz Cierpicki. "Targeting epigenetic protein–protein interactions with small-molecule inhibitors." Future Medicinal Chemistry 12, no. 14 (2020): 1305–26. http://dx.doi.org/10.4155/fmc-2020-0082.

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Epigenetic protein–protein interactions (PPIs) play essential roles in regulating gene expression, and their dysregulations have been implicated in many diseases. These PPIs are comprised of reader domains recognizing post-translational modifications on histone proteins, and of scaffolding proteins that maintain integrities of epigenetic complexes. Targeting PPIs have become focuses for development of small-molecule inhibitors and anticancer therapeutics. Here we summarize efforts to develop small-molecule inhibitors targeting common epigenetic PPI domains. Potent small molecules have been rep
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Li, Xiyan, Xin Wang, and Michael Snyder. "Systematic investigation of protein-small molecule interactions." IUBMB Life 65, no. 1 (2012): 2–8. http://dx.doi.org/10.1002/iub.1111.

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Luo, Fang, Gege Qin, Tie Xia, and Xiaohong Fang. "Single-Molecule Imaging of Protein Interactions and Dynamics." Annual Review of Analytical Chemistry 13, no. 1 (2020): 337–61. http://dx.doi.org/10.1146/annurev-anchem-091619-094308.

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Live-cell single-molecule fluorescence imaging has become a powerful analytical tool to investigate cellular processes that are not accessible to conventional biochemical approaches. This has greatly enriched our understanding of the behaviors of single biomolecules in their native environments and their roles in cellular events. Here, we review recent advances in fluorescence-based single-molecule bioimaging of proteins in living cells. We begin with practical considerations of the design of single-molecule fluorescence imaging experiments such as the choice of imaging modalities, fluorescent
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Dissertations / Theses on the topic "Protein-molecule interactions"

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Napoleon, Raeanne L. "Understanding small molecule-protein interactions." Thesis, Boston University, 2012. https://hdl.handle.net/2144/31592.

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Thesis (Ph.D.)--Boston University<br>PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.<br>The binding of small molecules to a protein is among the most important phenomena in the chemistry of life; the activity and functionality of many proteins depend critically on binding small molecules. A deep
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Albertoni, Barbara [Verfasser]. "Biophysical analysis of protein-protein and protein-small molecule interactions / Barbara Albertoni." Bonn : Universitäts- und Landesbibliothek Bonn, 2011. http://d-nb.info/1044846909/34.

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Jackson, Matthew. "Assay development and investigation of small molecule and amyloid protein interactions." Thesis, University of Sheffield, 2014. http://etheses.whiterose.ac.uk/6549/.

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Mittal, Sumit [Verfasser], Elsa [Gutachter] Sanchez-Garcia, and Simon [Gutachter] Ebbinghaus. "Small molecule modulation of protein-protein interactions / Sumit Mittal ; Gutachter: Elsa Sanchez-Garcia, Simon Ebbinghaus." Bochum : Ruhr-Universität Bochum, 2017. http://d-nb.info/1133361854/34.

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Pérez, González Daniel Cibrán. "Single-molecule studies of nucleic acid folding and nucleic acid-protein interactions." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/12039.

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Nucleic acids and proteins, some of the building blocks of life, are not static structures but highly dynamic entities that need to interact with one another to meet cellular demands. The work presented in this thesis focuses on the application of highly sensitive fluorescence methods, both at ensemble and single-molecule level, to determine the dynamics and structure of specific biomolecular interactions with nanometer resolution and in temporal scales from nanoseconds to minutes, which includes most biologically relevant processes. The main aims of my PhD can be classified in three areas: i)
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Fagiewicz, Robert Mateusz. "Structural analysis of protein-small molecule interactions by a crystallographic and spectroscopic approach." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2017. http://amslaurea.unibo.it/13892/.

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Modern spectroscopic techniques grant various methods for a protein structure determination among with a ligand interaction. This work aims at probing the structural insights of a protein-small molecule interaction with biocrystallography and optical spectroscopies. Two independent systems were investigated in the frame of this thesis. The first one involves flavoenzyme interaction with a natural nucleotide as a cofactor required for its catalytic activity and work was purely based on macromolecular crystallography. The second concerns incorporation of a synthetic fluorescent ligand into a mod
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Uphoff, Stephan. "Studying protein-DNA interactions in vitro and in vivo using single-molecule photoswitching." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:d0a52864-6d26-44a4-8fb7-5d12624a04ba.

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Protein-DNA interactions govern the fundamental cellular processes of DNA replication, transcription, repair, and chromosome organisation. Despite their importance, the detailed molecular mechanisms of protein-DNA interactions and their organisation in the cell remain elusive. The complexity of molecular biology demands new experimental concepts that resolve the structural and functional diversity of biomolecules. In this thesis, I describe fluorescence methods that give a direct view on protein-DNA interactions at the single-molecule level. These methods employ photoswitching to control the n
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Kung, Wei-Wei. "Protein-protein interactions and small molecule targeting of the multisubunit SOCS2-EloBC-Cul5-Rbx2 E3 ubiquitin ligase." Thesis, University of Dundee, 2018. https://discovery.dundee.ac.uk/en/studentTheses/b2dd4bc4-9a13-428b-a45a-bc46b1d9c116.

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The Cullin-RING E3 ligases (CRLs) are the largest subfamily of E3 ligases that participate in many biological processes determining the fate of proteins by catalysing ubiquitin transfer to specific substrates for proteasomal degradation. SOCS2 is a component of the multisubunit CRL E3 complex (CRL5SOCS2). SOCS2 plays important roles in several cancers and is involved in diabetes and inflammatory diseases. This work aims to understand the substrate recognition mechanism of SOCS2 at an atomic level and provides structural insights to guide the development of small-molecule tools and potential dr
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Krumm, Stefanie A. [Verfasser], and Dieter [Akademischer Betreuer] Wolf. "Protein-protein and protein-small-molecule inhibitor interactions in the measles virus replication complex / Stefanie A. Krumm. Betreuer: Dieter Wolf." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2015. http://d-nb.info/1069815470/34.

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Hofmann, Clemens. "Pigment pigment interactions and protein dynamics in light harvesting complexes a single molecule study /." [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=971750483.

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Books on the topic "Protein-molecule interactions"

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Waldmann, H., and M. Koppitz, eds. Small Molecule — Protein Interactions. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0.

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name, No. Small molecule-protein interactions. Springer, 2003.

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H, Waldmann, and Koppitz M. 1965-, eds. Small molecule--protein interactions. Springer, 2003.

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Vassilev, Lyubomir, and David Fry, eds. Small-Molecule Inhibitors of Protein-Protein Interactions. Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-17083-6.

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Armstrong, Megan Julia. Single molecule imaging to characterize protein interactions with the environment. [publisher not identified], 2019.

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Byun, Wan Gi. Discovery of Small-Molecule Modulators of Protein–RNA Interactions for Treating Cancer and COVID-19. Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-19-7814-2.

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Waldmann, Herbert, and Marcus Koppitz. Small Molecule - Protein Interactions. Springer, 2014.

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Waldmann, Herbert, and Marcus Koppitz. Small Molecule -- Protein Interactions. Springer London, Limited, 2013.

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Waldmann, Herbert. Small Molecule - Protein Interactions. Springer, 2012.

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Fry, David, and Lyubomir Vassilev. Small-Molecule Inhibitors of Protein-Protein Interactions. Springer London, Limited, 2011.

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Book chapters on the topic "Protein-molecule interactions"

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Reinhard-Rupp, J., and G. Wess. "Drug Discovery Opportunities." In Small Molecule — Protein Interactions. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_1.

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Briem, H. "De Novo Design Methods." In Small Molecule — Protein Interactions. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_10.

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Breinbauer, R., I. R. Vetter, and H. Waldmann. "From Protein Domains to Drug Candidates — Natural Products as Guiding Principles in Compound Library Design and Synthesis." In Small Molecule — Protein Interactions. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_11.

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Weber, L. "Discovery of New MCRs, Chemical Evolution and Lead Optimization." In Small Molecule — Protein Interactions. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_12.

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Hermkens, P. H. H., and G. Müller. "The Impact of Combinatorial Chemistry on Drug Discovery." In Small Molecule — Protein Interactions. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_13.

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Hopkins, A. L., and C. R. Groom. "Target Analysis: A Priori Assessment of Druggability." In Small Molecule — Protein Interactions. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_2.

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Wells, J., M. Arkin, A. Braisted, et al. "Drug Discovery at Signaling Interfaces." In Small Molecule — Protein Interactions. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_3.

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Willson, T. "Chemical Genomics of Orphan Nuclear Receptors." In Small Molecule — Protein Interactions. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_4.

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Jhoti, H. "High-Throughput X-Ray Techniques and Drug Discovery." In Small Molecule — Protein Interactions. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_5.

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Kessler, H., M. Heller, G. Gemmecker, T. Diercks, E. Planker, and M. Coles. "NMR in Medicinal Chemistry." In Small Molecule — Protein Interactions. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_6.

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Conference papers on the topic "Protein-molecule interactions"

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Púa, Lizeth Gutiérrez, Virginia Paredes Méndez, Ana María Fonseca Reyes, Juan Carlos Rincón Montenegro, and Lily Margareth Payares. "Enhanced Corrosion Resistance and Biocompatibility of Pure Magnesium Modified by Calcium Phosphate / Biomass of Chlorella Sp. Coating for Orthopedic Applications." In CONFERENCE 2022. AMPP, 2022. https://doi.org/10.5006/c2022-18513.

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Extended Abstract Biomedical metallic materials can be harmful to the human body in the long term due to the release and accumulation of metallic particles resulting from the degradation and corrosion of the material, a consequence of the wear suffered by the implant. Therefore, biodegradable materials have been studied that reduce the risk to health and the need for a second surgical intervention to remove the implant when the tissue is regenerated. Magnesium alloys are possible candidates as degradable biomaterials for temporary implants in various specialties such as traumatology, cardiolog
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Cisse, Ibrahim, Burak Okumus, Chirlmin Joo, and Taekjip Ha. "Single Molecule Studies of Protein-DNA Interactions inside Porous Nanocontainers." In Laser Science. OSA, 2008. http://dx.doi.org/10.1364/ls.2008.ltha4.

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Ameer-Beg, Simon M., Conor Treacy, Simon Poland, Justin Aluko, Thomas Kavanagh, and Michael Boersch. "Detection of protein-protein interactions within biological nano-domains by single molecule programmable array microscopy." In Multiphoton Microscopy in the Biomedical Sciences XXIV, edited by Ammasi Periasamy, Peter T. So, and Karsten König. SPIE, 2024. http://dx.doi.org/10.1117/12.3002714.

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Garini, Yuval. "Optical method for studying DNA-protein interactions at the single-molecule level." In Imaging Systems and Applications. OSA, 2013. http://dx.doi.org/10.1364/isa.2013.im3e.2.

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Kralj, Sebastjan, Milan Hodošček, Marko Jukić, and Urban Bren. "A comprehensive in silico protocol for fast automated mutagenesis and binding affinity scoring of protein-ligand complexes." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.674k.

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Protein-protein interactions (PPI) are critical for cellular functions, host-pathogen dynamics and are crucial with drug design efforts. The interaction of proteins is dependent on the amino acid sequence of a protein as it determines its binding affinity to various molecules, including drugs, DNA, RNA, and proteins. Polymorphisms, natural DNA variations, affect PPIs by altering protein structure and stability. Computational chemistry is vital for the prediction of ligand-protein interactions through techniques such as docking and molecular dynamics and can elucidate the changes in energy asso
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Fore, Samantha, Thomas Huser, Rod Balhorn, Monique Cosman, and Yin Yeh. "Application of Single Molecule FRET Photon-correlation Spectroscopy to Studying DNA-Protein Interactions." In Frontiers in Optics. OSA, 2005. http://dx.doi.org/10.1364/fio.2005.fwk6.

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Tseng, Fan-Gang. "From High Performance Protein Micro Chip Toward Ultra High Sensitive Single Molecule Nano Array." In ASME 2009 7th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2009. http://dx.doi.org/10.1115/icnmm2009-82291.

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Protein microarrays have been employed to screen tens to thousands of proteins simultaneously for the observation of the biochemical activities in the protein-protein, protein-nucleic acid and small molecule interactions. This technology allows high throughput analysis and holds great potential for basic molecular biology research, disease marker identification, toxicological response profiling and pharmaceutical target screening. However, proteins easily malfunction in harsh environments so that they are hardly preserved before the application because of their complex and fragile structures.
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Kesić, Ana S., Snežana R. Radisavljević, Jovana V. Bogojeski, and Biljana V. Petrović. "The interaction studies of novel diaminophenazine gold(III) complex and Bovine Serum Albumin (BSA-ibuprofen and BSA-Eozine Y)." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.407k.

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It is well known that gold(III) complexes have found applications in medicinal inorganic chemistry. Considering this, the right choice of inert ligands in the structure of Au(III) complexes is crucial for predicting their properties and reactivity, especially towards biomolecules. Here are presented the results of the study of the interactions between the new gold(III) complex [Au(DAP)Cl3], with 2,3-diaminophenazine (DAP) as an inert ligand, and BSA. Specifically, serum albumin is the main soluble protein in the circulatory system of humans. The metabolism of drugs, their distribution, free co
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Jongwan, Kim, Hocheol Lim, and K. T. No. "Abstract A45: In silico drug discovery targeting Hippo pathway and YAP-TEAD protein-protein interactions for small-molecule anticancer agent." In Abstracts: AACR Special Conference on the Hippo Pathway: Signaling, Cancer, and Beyond; May 8-11, 2019; San Diego, CA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1557-3125.hippo19-a45.

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Zheng, Zhuoyuan, Akash Singh, and Yumeng Li. "Molecular Dynamic Simulation Study on Soy Protein As Drug Delivery Vehicle." In ASME 2020 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2020. http://dx.doi.org/10.1115/imece2020-23590.

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Abstract Protein-based drug carriers are promising candidates for efficient drug delivery among the available potential colloidal carrier systems, due to their low cytotoxicity, abundance, renewability, diverse functional groups and interactions, and high drug loading capacity, etc. In this study, molecular dynamics (MD) simulations are performed to study the mechanisms of 11S molecule of soy protein as drug delivery vehicle to attach allyl isothiocyanate (AITC) and doxorubicin (DOX) drugs. The intermolecular interactions between protein and drugs are investigated; and the loading capacities o
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Reports on the topic "Protein-molecule interactions"

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Chamovitz, Daniel A., and Zhenbiao Yang. Chemical Genetics of the COP9 Signalosome: Identification of Novel Regulators of Plant Development. United States Department of Agriculture, 2011. http://dx.doi.org/10.32747/2011.7699844.bard.

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This was an exploratory one-year study to identify chemical regulators of the COP9 signalosome. Chemical Genetics uses small molecules to modify or disrupt the function of specific genes/proteins. This is in contrast to classical genetics, in which mutations disrupt the function of genes. The underlying concept is that the functions of most proteins can be altered by the binding of a chemical, which can be found by screening large libraries for compounds that specifically affect a biological, molecular or biochemical process. In addition to screens for chemicals which inhibit specific biologic
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Weiss, Shimon, and Xavier Michalet. Single-Molecule Methods for the Large-Scale Characterization of Expression Levels and Protein-Protein Interactions in Shewanella Oneidensis MR-1. Office of Scientific and Technical Information (OSTI), 2008. http://dx.doi.org/10.2172/1010284.

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Yedidia, I., H. Senderowitz, and A. O. Charkowski. Small molecule cocktails designed to impair virulence targets in soft rot Erwinias. United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134165.bard.

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Chemical signaling between beneficial or pathogenic bacteria and plants is a central factor in determining the outcome of plant-microbe interactions. Pectobacterium and Dickeya (soft rot Erwinias) are the major cause of soft rot, stem rot, and blackleg formed on potato and ornamentals, currently with no effective control. Our major aim was to establish and study specific bacterial genes/proteins as targets for anti-virulence compounds, by combining drug design tools and bioinformatics with experimental work. The approach allowed us to identify and test compounds (small molecules) that specific
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Tzfira, Tzvi, Michael Elbaum, and Sharon Wolf. DNA transfer by Agrobacterium: a cooperative interaction of ssDNA, virulence proteins, and plant host factors. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7695881.bard.

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Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand
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