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AVID: an integrative framework for discovering functional relationships among proteins

Taijiao Jiang, Amy E Keating
2005 BMC Bioinformatics  
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

Gennady Verkhivker
2022 International Journal of Molecular Sciences  
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

Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Rafii Yusop, Mahboobe Sadat Golestan Hashemi, Mohammad Hossein Nadimi Shahraki, Hamid Rastegari, Gous Miah, Farzad Aslani
2017 Biotechnology & Biotechnological Equipment  
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

Margaret E. Ackerman, Dan H. Barouch, Galit Alter
2017 Immunological Reviews  
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

Hong Zhang, Jinan Chen, Yongqiang Wang, Lin Peng, Xiaoxi Dong, Yi Lu, Amy E. Keating, Taijiao Jiang
2009 Journal of Molecular Biology  
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

Jianxin Wang, Min Li, Youping Deng, Yi Pan
2010 BMC Genomics  
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

Mohammed AlQuraishi, Grigoriy Koytiger, Anne Jenney, Gavin MacBeath, Peter K Sorger
2014 Nature Genetics  
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

Anne S De Groot, Lenny Moise, Rui Liu, Andres H Gutierrez, Ryan Tassone, Chris Bailey-Kellogg, William Martin
2014 Human Vaccines & Immunotherapeutics  
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

Anthony Levasseur, Pierre Pontarotti, Olivier Poch, Julie D. Thompson
2008 Evolutionary Bioinformatics  
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

Xuewu Liu, Yuxiao Huang, Jiao Liang, Shuai Zhang, Yinghui Li, Jun Wang, Yan Shen, Zhikai Xu, Ya Zhao
2014 BMC Bioinformatics  
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]

Marc R. Birtwistle, Jens Hansen, James M. Gallo, Sreeharish Muppirisetty, Peter Man-Un Ung, Ravi Iyengar, Avner Schlessinger
2016 Systems Pharmacology and Pharmacodynamics  
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

Jian Zhang, Peiyuan Wang, Lin Wan, Shouping Xu, Da Pang
2017 Autophagy  
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]

Jesper Tegnér, Francesco Marabita, David Gomez-Cabrero
2014 Between the Lines of Genetic Code  
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

Matthew J. Lazzara, Douglas A. Lauffenburger
2009 Experimental Cell Research  
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]

(:Unkn) Unknown, University, My, Ann M. Valentine
2020
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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