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Create and assess protein networks through molecular characteristics of individual proteins

Y. Ofran, G. Yachdav, E. Mozes, T.-t. Soong, R. Nair, B. Rost
2006 Bioinformatics  
combines the two levels by using the molecular characteristics to assess networks.  ...  Integrating molecular data and insights about the qualities of individual proteins into the analysis may enhance our ability to decipher biological pathways and processes.  ...  Yet, the molecular details of the individual proteins are crucial for understanding and assessing networks.  ... 
doi:10.1093/bioinformatics/btl258 pmid:16873500 fatcat:2tt454r4pfesbpbtykmzvs4m3y

Modeling of Protein Signaling Networks in Clinical Proteomics

D.H. GEHO, E.F. PETRICOIN, L.A. LIOTTA, R.P. ARAUJO
2005 Cold Spring Harbor Symposia on Quantitative Biology  
Within the field of cancer research, protein interaction networks play pivotal roles in the establishment and maintenance of the hallmarks of malignancy, including cell division, invasion, and migration  ...  Through this type of system, the effects of particular pharmacological agents may be used to test the effects of signal pathway inhibition or activation on multiple endpoints within a pathway.  ...  the divide between the molecular portrait of an individual patient's aberrant signaling network and an effective treatment.  ... 
doi:10.1101/sqb.2005.70.022 pmid:16869790 fatcat:rvrpvf32gnc4rc3nmmgrdxeqre

In Silico Prediction of a Multitope Vaccine against Moraxella catarrhalis: Reverse Vaccinology and Immunoinformatics

Mohamed A. Soltan, Nada Elbassiouny, Helmy Gamal, Eslam B. Elkaeed, Refaat A. Eid, Muhammad Alaa Eldeen, Ahmed A. Al-Karmalawy
2021 Vaccines  
These proteins were found to be essential, outer membrane, virulent and non-human homologs with appropriate molecular weight and high antigenicity score.  ...  For each protein, cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) and B cell lymphocyte (BCL) epitopes were predicted and confirmed to be highly antigenic and cover conserved regions of the proteins  ...  Molecular Docking of Vaccine with TLR2 ClusPro 2.0 was employed to perform protein-protein molecular docking between the subunit vaccine and TLR2 receptor, where 30 models were created and, among them,  ... 
doi:10.3390/vaccines9060669 pmid:34207238 pmcid:PMC8234879 fatcat:3vdz3jebvfeqtfdwpfpg3svs3y

Risk assessment, disease prevention and personalised treatments in breast cancer: is clinically qualified integrative approach in the horizon?

Olga Golubnitschaja, Kristina Yeghiazaryan, Vincenzo Costigliola, Daniela Trog, Michael Braun, Manuel Debald, Walther Kuhn, Hans H Schild
2013 The EPMA Journal  
The absolute necessity to create individual patient profiles and extended medical records is justified for the utilising by routine medical services.  ...  Actual paper shows that the elaboration of an integrative diagnostic approach combining several levels of examinations creates a robust platform for the reliable risk assessment, targeted preventive measures  ...  This "molecular portrait" creates an individual condition for the disease predisposition and promotion, which is recognisable and modifiable through individual pathology specific "molecular patterns".  ... 
doi:10.1186/1878-5085-4-6 pmid:23418957 pmcid:PMC3615949 fatcat:t7ytw7no55bl7bynvzxwzmq4y4

The Human Plasma Membrane Peripherome: Visualization and Analysis of Interactions

Katerina C. Nastou, Georgios N. Tsaousis, Kimon E. Kremizas, Zoi I. Litou, Stavros J. Hamodrakas
2014 BioMed Research International  
Moreover, functional and graph theory based analyses have been performed to assess biological features of the network.  ...  In conclusion, we reveal novel features and properties regarding the protein-protein interaction network created by peripheral proteins of the human plasma membrane.  ...  and Technology of the Greek Ministry of Education and Religious Affairs, Culture and Sports.  ... 
doi:10.1155/2014/397145 pmid:25057483 pmcid:PMC4095733 fatcat:w7t3n5hfuvbjnfry25dhv3ao5i

Systems Proteomics for Translational Network Medicine

D. K. Arrell, A. Terzic
2012 Circulation: Cardiovascular Genetics  
Sources of Funding The authors are supported by National Institutes of Health, Marriott Foundation, Fondation Leducq, and Mayo Clinic. Disclosures None.  ...  identification of nodes of interest and relevant network structural characteristics.  ...  Network medicine/biology Analysis of molecular (eg, protein, gene, metabolite) interaction networks through complex network theory, comprising topological features characterizing symmetric or asymmetric  ... 
doi:10.1161/circgenetics.110.958991 pmid:22896016 pmcid:PMC3466103 fatcat:hudrukaw5je4bfanb4hlcyjege

GPCRs Are Optimal Regulators of Complex Biological Systems and Orchestrate the Interface between Health and Disease

Hanne Leysen, Deborah Walter, Bregje Christiaenssen, Romi Vandoren, İrem Harputluoğlu, Nore Van Loon, Stuart Maudsley
2021 International Journal of Molecular Sciences  
condition long-term GPCR activities associated with the regulation of protein expression patterns, cellular stress responses and DNA integrity management.  ...  The molecular diversity of GPCR signaling systems is likely to be closely associated with disease-associated changes in organismal tissue complexity and compartmentalization, thus enabling a nuanced GPCR-based  ...  for individual patients with their unique molecular disease networks [84] .  ... 
doi:10.3390/ijms222413387 pmid:34948182 pmcid:PMC8708147 fatcat:kn7hrmgxojg6vp7u57edejuoh4

A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine

Serena Dotolo, Anna Marabotti, Anna Maria Rachiglio, Riziero Esposito Abate, Marco Benedetto, Fortunato Ciardiello, Antonella De Luca, Nicola Normanno, Angelo Facchiano, Roberto Tagliaferri
2021 Briefings in Bioinformatics  
The aim of this work is to define an innovative bioinformatics pipeline focused on the design and analysis of networks (such as biomedical and molecular networks), in order to: (1) improve the disease  ...  Results By using our pipeline based on a multiple network approach, it has been possible to demonstrate and validate what are the joint effects and changes of the molecular profile that occur in patients  ...  of a change at the molecular level, through the molecular analysis of the gene-gene network (reported in the Supplementary Data, Fig. 4a-b; ) and the protein-protein interaction network (reported in  ... 
doi:10.1093/bib/bbab180 pmid:34050359 pmcid:PMC8574709 fatcat:ehttzoido5enhmu37n4znn5wye

Proteomics and Systems Biology for Understanding Diabetic Nephropathy

Jonathan M. Starkey, Ronald G. Tilton
2012 Journal of Cardiovascular Translational Research  
The goal is to translate these new definitions into improved patient outcomes through diagnostic, prognostic and therapeutic tools.  ...  Novel technologies in mass spectrometry-based proteomics have the ability to provide a deeper understanding of the disease beyond classical histopathology, redefine the characteristics of the disease state  ...  An additional caveat is the observation that individually resolved spots may contain multiple distinct proteins of nearly identical molecular weight and pI, thus making protein quantification in that spot  ... 
doi:10.1007/s12265-012-9372-9 pmid:22581264 pmcid:PMC3410437 fatcat:s4sfeamt6nfpvpqfyk5jatvr5u

Alzheimer's disease under the purview of Graph Theory Centric Genetic Networks

Yegnanarayanan Venkatraman, Member, Board of Advisors, RNB Global University, Bikaner, Rajasthan - 334601, India, Narayanaa Y Krithicaa, Valentina E. Balas, Marius M. Balas, Department of Biomedical Sciences, Sri Ramachandra Institute for Higher Education and Research (Deemed to be University), Chennai, Tamil Nadu - 600116, India., Aurel Vlaicu University of Arad, Faculty of Engineering, Aurel Vlaicu University of Arad, Faculty of Engineering
2021 Brain: Broad Research in Artificial Intelligence and Neuroscience  
We then present some of the network-applied outcome in assessing the disease-signalling interactions, signal transduction of protein-protein interaction, disturbed genetics and signalling pathways as compelling  ...  It attempts to explain the connections and communication between networks of neurons.  ...  Acknowledgement This research was supported by the European Union through the European Regional Development Fund under the Competitiveness Operational Program (BioCell-NanoART = Novel Bio-inspired Cellular  ... 
doi:10.18662/brain/12.2/199 fatcat:d3maooxhcna7zjdk6gzplmmx6q

Systems Medicine and the Emergence of Proactive P4 Medicine [chapter]

Leroy Hood, Mauricio A. Flores, Kristin R. Brogaard, Nathan D. Price
2013 Handbook of Systems Biology  
The genetic, molecular, cellular, organ and individual networks are represented, and represent a fully integrated network of networks.  ...  In the organ-specific blood protein fingerprints each individual protein assesses the behavior of its cognate biological network, distinguishing normal functioning from disease-perturbed functioning by  ... 
doi:10.1016/b978-0-12-385944-0.00023-x fatcat:eunnctdrpzeytf6zjlqcxi3csq

A Bioinformatics Approach Toward Unravelling the Synaptic Molecular Crosstalk Between Alzheimer's Disease and Diabetes

Steven R. Alves, Cristóvão da Cruz e Silva, Ilka Martins, Ana Gabriela Henriques, Odete A.B. da Cruz e Silva
2022 Journal of Alzheimer's Disease  
Given the relevance of signaling pathways, another network was constructed focusing on protein kinases and protein phosphatases, and the top 6 kinase nodes (LRRK2, GSK3B, AKT1, EGFR, MAPK1, and FYN) were  ...  The interactome for each of these key proteins was retrieved and network maps were developed for AD and IS. Synaptic enrichment was performed to reveal synaptic common hubs.  ...  Categorical variables were assessed through examination of frequencies, while continuous variables were assessed through generation of descriptive (means, standard deviations) methods to investigate the  ... 
doi:10.3233/jad-215059 pmid:35253743 pmcid:PMC9108712 fatcat:v5rg66mjzjf4hg4732ecjciceq

Systems biology applied to heart failure with normal ejection fraction

Evandro Tinoco Mesquita, Antonio Jose Lagoeiro Jorge, Celso Vale de Souza Junior, João Paulo Pedroza Cassino
2014 Arquivos Brasileiros de Cardiologia  
Advances in the omics sciences and techniques of high data processing used in molecular biology have enabled the development of an integrating approach to HFNEF based on systems biology.  ...  A conceptual model was developed using bottom-up and top-down approaches of systems biology.  ...  Based on the advances of molecular biology and using the oslerian view, the identification of individual genes, proteins and cells has been sought, as well as the study of their functions, providing limited  ... 
pmid:24918915 pmcid:PMC4051455 fatcat:ijr426eblrelhey6es3tdh4uh4

Systematic and Integrative Analysis of Proteomic Data using Bioinformatics Tools

Rashmi Rameshwari, Dr. T.
2011 International Journal of Advanced Computer Science and Applications  
However, characteristics of individual metabolites have been neglected in this network.  ...  Network models have facilitated a shift from the study of evolutionary conservation between individual gene and gene products towards the study of conservation at the level of pathways and complexes.  ...  These characteristics are governed by physical and chemical properties of the proteins or other molecules involved, which may be actual molecules that have been described through extensive proteomics experiments  ... 
doi:10.14569/ijacsa.2011.020505 fatcat:dcp7gbrorja7lfmxsmbnumevde

Self-Organization of the Escherichia Coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy

Ann McEvoy, Derek Greenfield, Hari Shroff, Gavin E. Crooks, Ned S. Wingreen, Eric Betzig, Jan Liphardt
2010 Biophysical Journal  
Furthermore, we show that there is an intrinsic electromechanical heterogeneity in axial direction of individual fibrils that holds even for the collagen fibrils embedded in bone matrix.  ...  Such heterogeneity may have implications in regulating the ionic environment in bone responsible for bone remodeling. 3953-Plat SAXS: Structure Verification of an S-Layer Protein using a Fractal Mean Force  ...  Using a combination of SAXS and molecular dynamics simulations we get an integrated picture of the structure of S-layer proteins, for which no crystallized structure is currently available.  ... 
doi:10.1016/j.bpj.2009.12.4175 fatcat:4oa44vul7rhybizynzopi4qeeq
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