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AVID: an integrative framework for discovering functional relationships among proteins
2005
BMC Bioinformatics
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We present AVID, a computational method that uses a multi-stage learning framework to integrate experimental results with sequence information, generating networks reflecting functional similarities among ...
AVID provides three networks reflecting functional associations among proteins. ...
The AVID web site was developed by K. Weston. ...
doi:10.1186/1471-2105-6-136
pmid:15929793
pmcid:PMC1177925
fatcat:whcfjnx2nvfnbghgyfrynbbyxa
Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering
2022
International Journal of Molecular Sciences
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The analysis of computational studies is supplemented by an in-depth examination of mutational scanning simulations and identification of binding energy hotspots for distinct nanobody classes. ...
Recent research efforts on the design, protein engineering, and structure-functional characterization of nanobodies and their binding with SARS-CoV-2 S proteins reflected a growing realization that nanobody ...
The high avidity and long residence time typical for multivalent interactions are important for the biological function of nanobodies cocktails targeting SARS-CoV-2 S proteins. ...
doi:10.3390/ijms23062928
pmid:35328351
pmcid:PMC8951411
fatcat:ofwj5sfouvb5lb5uxrvstvnjuu
Intelligent mining of large-scale bio-data: Bioinformatics applications
2017
Biotechnology & Biotechnological Equipment
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Consequently, a challenging and valuable area for research in artificial intelligence has been created. ...
The present paper argues how artificial intelligence can assist bio-data analysis and gives an up-to-date review of different applications of bio-data mining. ...
Furthermore, the RenoDoI framework has been developed as an application to untangle huge and dense networks through DoI function, and has been integrated in the network visualization framework Cytoscape ...
doi:10.1080/13102818.2017.1364977
fatcat:qmbiss53wfggtc7ayj2ysgt5rq
Systems serology for evaluation of HIV vaccine trials
2017
Immunological Reviews
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Karen Dowell for figure preparation. ...
In sum, the integration of antibody feature and function data within an ML framework provides a new, objective approach to discovering and assessing multivariate immune correlates and hallmarks of highly ...
repeated exposure NHP challenge study; as well as to learn predictive relationships among features, such as estimations of effector function developed from antibody profiles. ...
doi:10.1111/imr.12503
pmid:28133810
pmcid:PMC5292205
fatcat:nrl2hz2cmfgllevtfbw2p53qfm
A Computationally Guided Protein-Interaction Screen Uncovers Coiled-Coil Interactions Involved in Vesicular Trafficking
2009
Journal of Molecular Biology
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Our method provides an efficient route to discovering new coiled-coil interactions and uncovers a number of associations that may have functional significance for vesicular trafficking. ...
The α-helical coiled coil is among the most common protein-interaction motifs, and proteins predicted to contain coiled coils participate in diverse biological processes. ...
Construction of protein networks The physical interaction data used for the analysis in Fig. 1c were obtained from DIP_CORE 55 60 AVID is a method for predicting functional relationships among ...
doi:10.1016/j.jmb.2009.07.006
pmid:19591838
fatcat:nnuw5dkguzghzbu6pamxzjq3eu
Recent advances in clustering methods for protein interaction networks
2010
BMC Genomics
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Many studies have shown that clustering protein interaction network is an effective approach for identifying protein complexes or functional modules, which has become a major research topic in systems ...
The predictions of protein functions and interactions based on modules will be covered. ...
Jiang and Keating [89] described the first integrative framework, named AVID which integrates experimental results with sequence information, for the discovery of functional relationships among proteins ...
doi:10.1186/1471-2164-11-s3-s10
pmid:21143777
pmcid:PMC2999340
fatcat:lanqlo4t3bclzhpfryztcbd5qq
A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks
2014
Nature Genetics
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We describe an analytical framework based on multiscale statistical mechanics that integrates genomic and biophysical data to model the human SH2-phosphoprotein network in normal and cancer cells. ...
Functional interpretation of genomic variation is critical to understanding human disease but it remains difficult to predict the effects of specific mutations on protein interaction networks and the phenotypes ...
G.M. is an employee of and shareholder in Merrimack Pharmaceuticals, Inc.; P.K.S. is also a stockholder in Merrimack and chair of its SAB. ...
doi:10.1038/ng.3138
pmid:25362484
pmcid:PMC4244270
fatcat:5ytrxiibtja7rb72t2qs4nixty
Immune camouflage: Relevance to vaccines and human immunology
2014
Human Vaccines & Immunotherapeutics
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De Groot with the figures for this manuscript and Sarah Beseme with the preparation of the manuscript and figures is sincerely appreciated. ...
Perhaps integrating Tregitopes into protein therapeutics will reduce their immunogenicity. 14 We also plan to scan protein therapeutics for pre-existing Tregitopes; our deimmunization programs would ...
Our group uses an integrated set of bioinformatics tools (iVAX) that have been extensively validated for antigen sequence analysis and vaccine design 3 to identify immunogenic signals encoded in pathogen ...
doi:10.4161/hv.36134
pmid:25483703
pmcid:PMC4514035
fatcat:xwli4zkzu5fs3ajzl5oc5tgkve
Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
2008
Evolutionary Bioinformatics
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Phylogenetic approaches provide a unique conceptual framework for performing comparative analyses of all this data, for propagating information between different systems and for predicting or inferring ...
We also discuss how evolutionary concepts and phylogeny-based inference strategies are now being exploited in order to understand the evolution and function of biological systems. ...
Acknowledgements We would like to thank the Réseau National des Génopoles and ANR (NT05-3_43837) for fi nancial support. ...
doi:10.4137/ebo.s597
fatcat:6wdircy25ferlhphyle72xn5le
Computational prediction of protein interactions related to the invasion of erythrocytes by malarial parasites
2014
BMC Bioinformatics
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Results of network analysis suggest that SNARE proteins of parasites and APP of humans may function in the invasion of RBCs by parasites. ...
Although several interactions between human and parasite proteins have been discovered, the mechanism related to invasion remains poorly understood because numerous human-parasite protein interactions ...
For example, Date et al. utilized a Bayesian framework to integrate different data sources, including polygenetic profiles, gene expression profiles, and Rosetta stone fusion genes [10] . ...
doi:10.1186/s12859-014-0393-z
pmid:25433733
pmcid:PMC4265449
fatcat:na3stp4nuvhbbbd6f277kliw3u
Systems Pharmacology: An Overview
[chapter]
2016
Systems Pharmacology and Pharmacodynamics
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Networks of protein-protein interactions that were confirmed by experimental and computational analysis of the structure of the interaction partners can be combined with graph theory to identify modules ...
The integration of high-throughput data technologies with computational data analysis and modeling offers new opportunities to overcome the one disease, one target, one drug approach. ...
The integration of systems biology with pharmacology has given rise to the new field of systems pharmacology that provides an intellectual framework to consider complex physiology, pathophysiology, and ...
doi:10.1007/978-3-319-44534-2_4
fatcat:hnkzgvppa5ehjcqj65vw43fily
The emergence of noncoding RNAs as Heracles in autophagy
2017
Autophagy
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Then, we integrate public resources to predict autophagy-related noncoding RNAs across species and discuss strategies for and the challenges of identifying autophagyrelated noncoding RNAs. ...
This article will deepen our understanding of the relationship between noncoding RNAs and autophagy, and provide new insights to specifically target noncoding RNAs in autophagy-associated therapeutic strategies ...
Acknowledgments We thank Professors Hongbo Liu for assistance with figure preparation, critical reading of the manuscript and document submission. ...
doi:10.1080/15548627.2017.1312041
pmid:28441084
pmcid:PMC5486373
fatcat:z2f2zjwt7ndltgi6or7ifunwku
Network Biology Empowering Detection and Understanding of Interactions Between Genetic Factors in Development of Complex Phenotypes
[chapter]
2014
Between the Lines of Genetic Code
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NETWORK BIOLOGY-A FRAMEWORK FOR DETECTING GENETIC INTERACTIONS How to incorporate prior knowledge in a general statistical framework is still an unsolved problem. ...
In part due to these shortcomings of integrating several data types into an unbiased framework based on directly identifying biological networks directly from data, integrative bioinformatics techniques ...
doi:10.1016/b978-0-12-397017-6.00010-6
fatcat:smxdhm56mnhufireuz24cn775q
Quantitative modeling perspectives on the ErbB system of cell regulatory processes
2009
Experimental Cell Research
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This new data provides significant new insight, while at the same time creating new challenges for making quantitative statements and predictions with certainty. ...
processes involved in ErbB-mediated regulation of cellular phenotype are broadly appreciated, so much so that it might be reasonably argued that this highly studied system provided significant impetus for ...
ACKNOWLEDGEMENTS This work was partially supported by NCI Integrative Cancer Biology Program grant U54-CA112967 and NCI grant R01-CA096504. ...
doi:10.1016/j.yexcr.2008.10.033
pmid:19022246
fatcat:rvlvpqrykvhcfne67s4k3ralv4
INTERACTIONS OF ENTEROBACTIN AND RELATED MOLECULES WITH TITANIUM(IV): CHARACTERIZATION AND CONSEQUENCES OF AVID BINDING
[article]
2020
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Titanium(IV) (the most common oxidation state of titanium) also has a larger charge to size ratio than Fe(III) and may outcompete iron for binding. ...
The strongest siderophore to date is enterobactin (ent) which forms a Fe-ent complex with an association constant of 1049. ...
Speciation plot of the tiron and ent competition for Ti(IV
and metal ion delivery into even avid binding proteins like transferrin can take hours. 35 Despite the very strong affinity ent has for Ti( ...
doi:10.34944/dspace/2981
fatcat:id2yudkjgbblvdqt3nkaqknqje
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