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General principles of binding between cell surface receptors and multi-specific ligands: A computational study

Jiawen Chen, Steven C. Almo, Yinghao Wu, Alexandre V Morozov
<span title="2017-10-10">2017</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
OPEN ACCESS Citation: Chen J, Almo SC, Wu Y (2017) General principles of binding between cell surface receptors and multi-specific ligands: A computational study.  ...  We present a new coarse-grained model to realistically simulate the binding process between multi-specific ligands and membrane receptors on cell surfaces.  ...  Computational simulations were performed at the Albert Einstein College of Medicine High Performance Computing Center. Binding of multi-specific ligands  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1005805">doi:10.1371/journal.pcbi.1005805</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29016600">pmid:29016600</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5654264/">pmcid:PMC5654264</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ilb7aofh45antaqv2hdteyw3xm">fatcat:ilb7aofh45antaqv2hdteyw3xm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719162701/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005805&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fb/f4/fbf495bb4d0c95e9a2bf26f1273dd7e9ed5a4394.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1005805"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654264" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ligand-receptor interactions

Pierre Bongrand
<span title="1999-01-01">1999</span> <i title="IOP Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/suaksh5g2jbv7n457hrsdmxhuy" style="color: black;">Reports on progress in physics (Print)</a> </i> &nbsp;
The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems.  ...  First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by  ...  bind to specific receptors scattered through the cells (Bongrand and Malissen, 1998) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/0034-4885/62/6/202">doi:10.1088/0034-4885/62/6/202</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fw7agwebwvdazhgdxl7g7biw3u">fatcat:fw7agwebwvdazhgdxl7g7biw3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170927151352/https://hal.archives-ouvertes.fr/hal-00320498/document" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b0/6a/b06aa264e967d708dc8c63b7681a1da33a7fb520.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/0034-4885/62/6/202"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> iop.org </button> </a>

Multivalency in Ligand Design [chapter]

Vijay M. Krishnamurthy, Lara A. Estroff, George M. Whitesides
<span title="2006-08-28">2006</span> <i title="Wiley-VCH Verlag GmbH &amp; Co. KGaA"> Methods and Principles in Medicinal Chemistry </i> &nbsp;
binding to a surface ( N = unknown, M = i = 2), (e) a polymer binding to a surface (N = unknown, M = 8, i = 4), and (f) a dend'rirner bind-) , = receptor 4 = ligand I = linker ing to a surface ( N = unknown  ...  ligand binding to a protein with two different kinds of binding sites ( N = M = i = 2), (c) a tetravalent ligand binding to a tetravalent receptor (oligovalent) (N = M = i = 4), (d) a bivalent antibody  ...  Surfice Assays Using Purified Components (Cell-free Assays) e are several other techniques (e. g., ELISA) for measuring binding of multi-' t ligands or receptors to surfaces using in vitro assays [8, 32  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/3527608761.ch2">doi:10.1002/3527608761.ch2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oyewdjlwnzgk5pitmrh3dpng64">fatcat:oyewdjlwnzgk5pitmrh3dpng64</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20111208173136/http://gmwgroup.harvard.edu/pubs/pdf/963.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0f/d2/0fd2eb890e3382fb9aa9c070178c41290240547f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/3527608761.ch2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

A Tunable Coarse-Grained Model for Ligand-Receptor Interaction

Teresa Ruiz-Herrero, Javier Estrada, Raúl Guantes, David G. Miguez, Alexander Donald MacKerell
<span title="2013-11-14">2013</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Molecular dynamics simulations of chimeric ligands are used to study how selectivity can be optimized based on receptor abundance, ligand-receptor affinity and length of the linker between both ligand  ...  Cell-surface receptors are the most common target for therapeutic drugs.  ...  As a case study, the model is applied to the analysis of the binding properties of generic chimeric ligands, where we show how cell specificity is achieved and how it depends on receptor diffusion and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1003274">doi:10.1371/journal.pcbi.1003274</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24244115">pmid:24244115</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3828130/">pmcid:PMC3828130</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qruhpvqy4zbrbhjj6p5wcp2scm">fatcat:qruhpvqy4zbrbhjj6p5wcp2scm</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3828130/PMC3828130-journal.pcbi.1003274.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1d/da/1dda801c0b7e5cd7b0dd8ab21e719ad4e22ab18b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1003274"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828130" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Extracellular pH and Regulation of Integrin-Ligand Interactions

Ranjani Krishnan, Douglas A. Lauffenburger, Krystyn J. Van Vliet
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
J., 97. 210-Pos Computational Prediction and Experimental Validation of a Novel Binding Site for Platelet Integrin AlphaIIb-Beta3  ...  Six 3, 4 and 3,4-deoxy dimannose analogs were studied as ligands of the m4-P51G-CVN mutant of the potent anti-HIV carbohydrate binding agent Cyanovirin-N (1).  ...  Here, we consider the hypothesis that acidic extracellular pH directly alters the interactions between cell surface integrin receptors and ECM ligands, which are critical to cell adhesion and migration  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2009.12.231">doi:10.1016/j.bpj.2009.12.231</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7jnjg7kz2vcdxbshz3izownd7u">fatcat:7jnjg7kz2vcdxbshz3izownd7u</a> </span>
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A quantitative view of strategies to engineer cell-selective ligand binding [article]

Cyrillus Tan, Brian Orcutt-Jahns, Aaron Samuel Meyer
<span title="2020-11-27">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Therefore, guiding strategies for developing cell-specific binding are critical to employ these tools. Here, we extend a multi-valent binding model to multi-ligand and multi-receptor interactions.  ...  A critical property of many therapies is their selective binding to specific target populations. Exceptional specificity can arise from high-affinity binding to unique cell surface targets.  ...  c binding using a multi-valent, multi-receptor, multi-ligand binding model.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.25.398974">doi:10.1101/2020.11.25.398974</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3padg4klencvnng4yvcg3hjqzm">fatcat:3padg4klencvnng4yvcg3hjqzm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429135622/https://www.biorxiv.org/content/biorxiv/early/2020/11/27/2020.11.25.398974.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/04/80/04806fd3e6a030fda68ec3e9db4688ed39a34226.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.25.398974"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Stochastic models of receptor oligomerization by bivalent ligand

Tomás Alarcón, Karen M. Page
<span title="2006-02-28">2006</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kdv34qlmv5gsfphm6vnme655ia" style="color: black;">Journal of the Royal Society Interface</a> </i> &nbsp;
In this paper, we develop stochastic models of receptor binding by a bivalent ligand.  ...  A detailed kinetic study allows us to analyse the role of cross-linking in cell activation by receptor oligomerization.  ...  A further assumption is needed, namely, that ligand concentration specificity (i.e. the cell responds only to a narrow range of values of the ligand concentration) is a 'receptor design principle'.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2006.0116">doi:10.1098/rsif.2006.0116</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16849251">pmid:16849251</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1664659/">pmcid:PMC1664659</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/px3lir3yvrbobjvwpibisex45u">fatcat:px3lir3yvrbobjvwpibisex45u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808204953/http://www.ucl.ac.uk/~ucackmp/Publications_files/tomasreceptor.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/de/50/de50b1eb5ff059ca0f040202a7b6c00fd7f89c3e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2006.0116"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664659" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ligand-receptor promiscuity enables cellular addressing [article]

Christina J. Su, Arvind Murugan, James M. Linton, Akshay Yeluri, Justin Bois, Heidi Klumpe, Yaron E. Antebi, Michael B. Elowitz
<span title="2020-12-09">2020</span> <i title="Cold Spring Harbor Laboratory"> biorxiv/medrxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We find that promiscuously interacting ligand-receptor systems allow a small number of ligands, acting in combinations, to address a larger number of individual cell types, each defined by its receptor  ...  Key cell-cell communication pathways use multiple promiscuously interacting ligands and receptors, provoking the question of how addressing specificity can emerge from molecular promiscuity.  ...  C.J.S. is supported by the NIH National Institute of General Medical Sciences (grant T32 GM008042) and a David Geffen  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.12.08.412643">doi:10.1101/2020.12.08.412643</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/plirlskn6jgxlgzkq7i7ej6mda">fatcat:plirlskn6jgxlgzkq7i7ej6mda</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427203104/https://authors.library.caltech.edu/107015/1/2020.12.08.412643v1.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/dc/2a/dc2ab9e82b580002dc55bc904b32f910e9c10196.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.12.08.412643"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Evaluating apoenzyme–coenzyme–substrate interactions of methane monooxygenase with an engineered active site for electron harvesting: a computational study

Sikai Zhang, Raghupathy Karthikeyan, Sandun D. Fernando
<span title="2018-11-29">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/45p53qd7nrhxteu6rfvh5pcqay" style="color: black;">Journal of Molecular Modeling</a> </i> &nbsp;
This work was geared toward performing a structural analysis to identify the spatial distribution of FAD binding site(s) in correlation to Nicotinamide Adenine Dinucleotide (NAD) and subsequently to evaluate  ...  The overall goal of this work was to computationally evaluate the feasibility of attaching MMOs to a metal electrode and evaluate its functionality using docking and molecular dynamic (MD) simulations.  ...  Fernando, and my co-chair, Dr. Karthikeyan, and committee member Dr. Gomes for their inspiration and advice that guided me throughout the course of this research.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00894-018-3876-4">doi:10.1007/s00894-018-3876-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30498917">pmid:30498917</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2dqaoemwyfdxvp5tbubsn4bbby">fatcat:2dqaoemwyfdxvp5tbubsn4bbby</a> </span>
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A Force Spectroscopy-Based Protein-Ligand Interaction Assay

Yi Cao, Kai Shih Er, Rakesh Parhar, Hongbin Li
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
J., 97. 210-Pos Computational Prediction and Experimental Validation of a Novel Binding Site for Platelet Integrin AlphaIIb-Beta3  ...  Six 3, 4 and 3,4-deoxy dimannose analogs were studied as ligands of the m4-P51G-CVN mutant of the potent anti-HIV carbohydrate binding agent Cyanovirin-N (1).  ...  Here, we consider the hypothesis that acidic extracellular pH directly alters the interactions between cell surface integrin receptors and ECM ligands, which are critical to cell adhesion and migration  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2009.12.233">doi:10.1016/j.bpj.2009.12.233</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7fklli25svhd3nwwhx7wm7opny">fatcat:7fklli25svhd3nwwhx7wm7opny</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171004094815/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/dd3/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDAwNjM0OTUwOTAyMDM4NA%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5b/be/5bbe81cf24a1c05e871491c35c2d0166ebb2e38c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2009.12.233"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Changing Paradigm from one Target one Ligand Towards Multi-target Directed Ligand Design for Key Drug Targets of Alzheimer Disease: An Important Role of In Silico Methods in Multi-target Directed Ligands Design

Akhil Kumar, Ashish Tiwari, Ashok Sharma
<span title="2018-06-08">2018</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4puludp4rrgqjn6gqz5233oagy" style="color: black;">Current Neuropharmacology</a> </i> &nbsp;
Moreover, multi-target AD drug discovery added extra challenges such as the good binding affinity of ligands for multiple targets, optimal ADME/T properties, no/less off-target side effect and crossing  ...  Moreover, we focused on ligand and structure-based computational approach to design MTDL against AD.  ...  Binding affinity and binding mode between vitamin K3 analogue and Aβ were studied by docking and MD simulation [48] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1570159x16666180315141643">doi:10.2174/1570159x16666180315141643</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29542413">pmid:29542413</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6080096/">pmcid:PMC6080096</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ylxayop3d5afzboa7eytazyj64">fatcat:ylxayop3d5afzboa7eytazyj64</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308151859/http://pdfs.semanticscholar.org/f536/fc61abd44a78ebf98159a3078e3b0468a897.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f5/36/f536fc61abd44a78ebf98159a3078e3b0468a897.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1570159x16666180315141643"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6080096" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A computational study of liposome logic: towards cellular computing from the bottom up

James Smaldon, Francisco J. Romero-Campero, Francisco Fernández Trillo, Marian Gheorghe, Cameron Alexander, Natalio Krasnogor
<span title="2010-07-18">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/quz6vpzkkrep7mfejluwmagkra" style="color: black;">Journal of Systems and Synthetic Biology</a> </i> &nbsp;
The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of "bottom-up" liposome logic.  ...  This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells.  ...  : A Synthetic Biology Network for Modelling and Programming Cell-Chell Interactions'' (BB/F01855X/1).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11693-010-9060-5">doi:10.1007/s11693-010-9060-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21886681">pmid:21886681</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2955200/">pmcid:PMC2955200</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e4p5m7o7ajeyrf2wl66oufzbvy">fatcat:e4p5m7o7ajeyrf2wl66oufzbvy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208081933/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2955200&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7e/41/7e4126835666f7c2c5c3e5fab0144f3890818dd8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11693-010-9060-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955200" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ligand binding by PDZ domains

Celestine N. Chi, Anders Bach, Kristian Strømgaard, Stefano Gianni, Per Jemth
<span title="2012-06-07">2012</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/el6uunw6unb2pfwsz5nhpuf7ya" style="color: black;">Biofactors</a> </i> &nbsp;
Ligand binding by PDZ domains. Biofactors, 38(5): 338-348 http://dx.  ...  PDZ domains generally bind the C-terminus of target proteins in a shallow pocket between the β2 strand and the α2 helix ( Fig. 1) (5, 6) .  ...  The mechanisms of binding and selectivity of PDZ domain and phosphoinositol ligands are generally poorly understood.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/biof.1031">doi:10.1002/biof.1031</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22674855">pmid:22674855</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tvh65xy2obgiphjcov5nwitjt4">fatcat:tvh65xy2obgiphjcov5nwitjt4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922013849/http://uu.diva-portal.org/smash/get/diva2:575739/FULLTEXT01" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8e/bb/8ebb7026f505ab9f8f4576bfda9fb6438277a1a2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/biof.1031"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Multidrug resistance protein P-gp interaction with nanoparticles (fullerenes and carbon nanotube) to assess their drug delivery potential: a theoretical molecular docking study

Sergey Shityakov, Carola Förster
<span title="">2013</span> <i title="Inderscience Publishers"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wo25vr36jnehrd7xlamyeoiozi" style="color: black;">International Journal of Computational Biology and Drug Design</a> </i> &nbsp;
drug delivery potential: a theoretical molecular docking study', Int.  ...  Furthermore, the SWCNT binding is energetically unfavorable, leading to a total decrease in binding affinity by elevation of the residual area (A res ), which also affects the π-π stacking mechanisms.  ...  The authors are grateful to the IZKF (Interdisziplinäres Zentrum für Klinische Forschung der Universität Würzburg) and the BMBF (Bundesministerium für Bildung und Forschung) for the support of this work  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1504/ijcbdd.2013.056801">doi:10.1504/ijcbdd.2013.056801</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24088267">pmid:24088267</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t57zp6slr5dnbawvcipgyx67de">fatcat:t57zp6slr5dnbawvcipgyx67de</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220224321/http://pdfs.semanticscholar.org/2946/2e76ff2a65c9106f5577617eda2723038787.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/29/46/29462e76ff2a65c9106f5577617eda2723038787.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1504/ijcbdd.2013.056801"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Polymer-tethered ligand–receptor interactions between surfaces

Jeremy I. Martin, Cheng-Zhong Zhang, Zhen-Gang Wang
<span title="">2006</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r2btjjalarcwhc3bsi64urfsia" style="color: black;">Journal of Polymer Science Part B: Polymer Physics</a> </i> &nbsp;
They examined the binding of mono- and multi-valent ligands, and specifically studied the difference between surfaces fully covered by recep- tors and those carrying fixed number of immobile, regularly  ...  The direct interaction between a ligand and a receptor is typically specific, i.e., it acts only between specific pairs of molecules or residues on molecules, and is short-ranged.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/polb.20897">doi:10.1002/polb.20897</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dy7nanzjofbeveyixfpywspkvq">fatcat:dy7nanzjofbeveyixfpywspkvq</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/details/sim_journal-of-polymer-science-part-b-polymer-physics_2006-09-15_44_18/page/2621" title="read fulltext microfilm" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Archive [Microfilm] <div class="menu fulltext-thumbnail"> <img src="https://archive.org/serve/sim_journal-of-polymer-science-part-b-polymer-physics_2006-09-15_44_18/__ia_thumb.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/polb.20897"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>
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