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Protein-protein Interactions: Network Analysis and Applications in Drug Discovery

Jennyfer Bultinck, Sam Lievens, Jan Tavernier
2012 Current pharmaceutical design  
An essential starting point for PPI inhibitor screening or design projects is the generation of a detailed map of the human interactome and the interactions between human and pathogen proteins.  ...  However, other genetic and biochemical methods will be essential to increase both coverage and resolution of current protein networks in order to increase their utility towards the identification of novel  ...  Table 2 lists a number of disease genes and pathways predicted from PPI network analysis in a wide range of pathologies.  ... 
doi:10.2174/138161212802651562 pmid:22650261 fatcat:stmuugvrljag7hgwididdign64

Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes

Domenico Scaramozzino, Gianfranco Piana, Giuseppe Lacidogna, Alberto Carpinteri
2021 International Journal of Molecular Sciences  
Elastic network models (ENMs) have been widely used to predict protein dynamics, flexibility and the biological mechanism, from which remarkable results have been found regarding the prediction of protein  ...  network (i.e., by considering a linear response theory).  ...  interactions in a simplified manner.  ... 
doi:10.3390/ijms221910501 pmid:34638837 pmcid:PMC8508695 fatcat:5giymbg6hvfs7odahim7uaw7me

The mechanism of coupled folding-upon-binding of an intrinsically disordered protein [article]

Paul Robustelli, Stefano Piana, David E. Shaw
2020 bioRxiv   pre-print
IDPs often fold into ordered states upon binding to their physiological interaction partners (a so-called "folding-upon-binding" process), but it has proven difficult to obtain an atomic-level description  ...  nucleoprotein (NTAIL) and the X domain (XD) of the measles virus phosphoprotein complex.  ...  ., Szabo, A. (2009) Reactive flux and folding pathways in network models of coarse-grained protein dynamics. J Chem Phys 130:205102. 31.  ... 
doi:10.1101/2020.03.23.004283 fatcat:mlsmx2nvjvggleykmurpj3axiq

Computational quantification of global effects induced by mutations and drugs in signaling networks of colorectal cancer cells [article]

Sara Sommariva, Giacomo Caviglia, Silvia Ravera, Francesco Frassoni, Federico Benvenuto, Lorenzo Tortolina, Nicoletta Castagnino, Silvio Parodi, Michele Piana
2020 bioRxiv   pre-print
The model can quantify the alteration in the concentration of the proteins connected with the examined mutation.  ...  Colorectal cancer (CRC) is one of the most deadly and commonly diagnosed tumors worldwide. Several genes are involved in its development and progression.  ...  Acknowledgment S.S. kindly acknowledges the AIRC grant COENzYME: "Chemotherapy effect On cell ENergY Metabolism and Endoplasmic reticulum redox control".  ... 
doi:10.1101/2020.12.30.424842 fatcat:ui4ddn7hazgfdalzpbioznjvd4

Role of Conformational Fluctuations in the Enzymatic Reaction of HIV-1 Protease

Stefano Piana, Paolo Carloni, Michele Parrinello
2002 Journal of Molecular Biology  
The role of conformational diversity in enzyme catalysis has been a matter of analysis in recent studies.  ...  Subtle nanosecond-timescale rearrangements in the active site hydrogen bonding network were shown to determine which reaction the enzyme follows. We named this phenomenon chemical disorder.  ...  , and multiple linear regression analysis.  ... 
doi:10.1016/s0022-2836(02)00301-7 pmid:12051929 fatcat:fu4sb66vmvgidif3jbny7vsklm

Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

Lorenzo Sborgi, Abhinav Verma, Stefano Piana, Kresten Lindorff-Larsen, Michele Cerminara, Clara M. Santiveri, David E. Shaw, Eva de Alba, Victor Muñoz
2015 Journal of the American Chemical Society  
Our results on gpW indicate that the methods employed in this study are likely to prove broadly applicable to the fine analysis of folding mechanisms in fast folding proteins.  ...  Experiments and simulations expose a remarkably complex pattern of structural changes that occur at the atomic level and from which the detailed network of residue−residue couplings associated with cooperative  ...  These complex interaction networks hold the key to folding mechanisms 2 and the rational design of new protein folds. 3 Folding interaction networks are, however, extremely elusive.  ... 
doi:10.1021/jacs.5b02324 pmid:25924808 pmcid:PMC4648500 fatcat:hyk2qzqsazesxdvwzg64gnlz4m

Overview of radiomics in breast cancer diagnosis and prognostication

Alberto Stefano Tagliafico, Michele Piana, Daniela Schenone, Rita Lai, Anna Maria Massone, Nehmat Houssami
2019 Breast  
Recent technological advances in medical imaging, especially in the field of artificial intelligence applied to image analysis, hold promise in addressing clinical challenges in cancer detection, assessment  ...  In this article we focus on the role and potential of radiomics in breast cancer diagnosis and prognostication.  ...  In addition, the biology of cancer is complex: cancer is a selfsustaining and adaptive process interacting dynamically with its microenvironment, which continues to challenge researchers, and clinicians  ... 
doi:10.1016/j.breast.2019.10.018 pmid:31739125 pmcid:PMC7375670 fatcat:igng3g4qenh55om6rap5tcgmye

Gain and Loss of Function mutations in biological chemical reaction networks: a mathematical model with application to colorectal cancer cells [article]

Sara Sommariva, Giacomo Caviglia, Michele Piana
2020 arXiv   pre-print
This paper studies a system of Ordinary Differential Equations modeling a chemical reaction network and derives from it a simulation tool mimicking Loss of Function and Gain of Function mutations found  ...  More specifically, from a theoretical perspective, our approach focuses on the determination of moiety conservation laws for the system and their relation with the corresponding stoichiometric surfaces  ...  Silvia Ravera and Dr. Mara Scussolini for their useful comments and feedback.  ... 
arXiv:2004.02632v1 fatcat:ucb7fopnirb5lgmnlom44jqcri

Identification of novel biomarkers associated with poor patient outcomes in invasive breast carcinoma

Renata A. Canevari, Fabio A. Marchi, Maria A. C. Domingues, Victor Piana de Andrade, José R. F. Caldeira, Sergio Verjovski-Almeida, Silvia R. Rogatto, Eduardo M. Reis
2016 Tumor Biology  
Ingenuity Pathway Analysis (IPA v8.0, Ingenuity® Systems, Redwood City, CA, USA; http://www.ingenuity. com) was used to identify the enriched pathways and biological interaction networks of the differentially  ...  The tumor suppressor gene PHB (prohibitin) encodes an anti-proliferative protein that functions by interacting with the Rb protein and its family members.  ... 
doi:10.1007/s13277-016-5133-8 pmid:27485113 fatcat:envw3gbwozf2hb3h3pyammlxgm

Gain and loss of function mutations in biological chemical reaction networks: a mathematical model with application to colorectal cancer cells

Sara Sommariva, Giacomo Caviglia, Michele Piana
2021 Journal of Mathematical Biology  
AbstractThis paper studies a system of Ordinary Differential Equations modeling a chemical reaction network and derives from it a simulation tool mimicking Loss of Function and Gain of Function mutations  ...  More specifically, from a theoretical perspective, our approach focuses on the determination of moiety conservation laws for the system and their relation with the corresponding stoichiometric surfaces  ...  as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.  ... 
doi:10.1007/s00285-021-01607-0 pmid:33945019 pmcid:PMC8096774 fatcat:qjb2y2dgb5hbtfbxw24ypzsqvy

Integration and Prediction of PPI Using Multiple Resources from Public Databases

Ramón Aragues, Javier García-García, Baldo Oliva
2008 Journal of Proteomics & Bioinformatics  
We find that the integrated network of interactions shows properties very similar to those observed in previously reported protein interaction networks.  ...  This integrative approach has been implemented into PIANA, a protein-protein interaction software framework under the GNU Public License (http://sbi.imim.es/piana).  ...  Acknowledgements We thank members of the UPF-IMIM SBI lab and P. Boixeda for their helpful comments. R.A is supported by a grant from the Spanish Ministerio de Ciencia y Tecnología  ... 
doi:10.4172/jpb.1000023 fatcat:ilajnuvp6ncvleeyivu2b3fmza

Gain and Loss of Function mutations in biological chemical reaction networks: a mathematical model with application to colorectal cancer cells [article]

Sara Sommariva, Giacomo Caviglia, Michele Piana
2020 bioRxiv   pre-print
This paper studies a system of Ordinary Differential Equations modeling a chemical reaction network and derives from it a simulation tool mimicking Loss of Function and Gain of Function mutations found  ...  More specifically, from a theoretical perspective, our approach focuses on the determination of moiety conservation laws for the system and their relation with the corresponding stoichiometric surfaces  ...  Silvia Ravera and Dr. Mara Scussolini for their useful comments and feedback.  ... 
doi:10.1101/2020.04.07.029439 fatcat:acqui2ul3rcqlnhfngsbqbyhke

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

Stefano Piana, John L Klepeis, David E Shaw
2014 Current Opinion in Structural Biology  
In Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (SC09). New York, NY: ACM; 2009, . 42.  ...  Piana S, Lindorff-Larsen K, Shaw DE: Protein folding kinetics and thermodynamics from atomistic simulation. Proc Natl Acad Sci U S A 2012, 109:17845-17850.  ... 
doi:10.1016/j.sbi.2013.12.006 pmid:24463371 fatcat:vybd3cq3nzc2zohm5n6njjwn3i

SARS-COV-2 comorbidity network and outcome in hospitalized patients in Crema, Italy

Tommaso Gili, Giampaolo Benelli, Elisabetta Buscarini, Ciro Canetta, Giuseppe La Piana, Guido Merli, Alessandro Scartabellati, Giovanni Viganò, Roberto Sfogliarini, Giovanni Melilli, Roberto Assandri, Daniele Cazzato (+7 others)
2021 PLoS ONE  
Comorbidity network analysis revealed a more homogenous distribution 60–40 aged SARS-COV-2 patients across diseases and a crucial different interplay of diseases in the networks of deceased and survived  ...  Non-invasive respiratory support rate was 27.2% and ICU admission 6.8%. Charlson comorbidity index and high C-reactive protein at admission were significantly associated with death.  ...  Acknowledgments We are deeply indebted with all the nurses of the Hospital of Crema, whose passion, skills and fortitude in taking care of patients was a bastion to limit the wave of suffering that in  ... 
doi:10.1371/journal.pone.0248498 pmid:33765013 fatcat:u6tur7t735bdrhvtn4dsvoomgy

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

Fabrizio Marinelli, Fabio Pietrucci, Alessandro Laio, Stefano Piana, Vijay S. Pande
2009 PLoS Computational Biology  
The model also predicts the presence of a state at C a -RMSD of 4.4 Å from the NMR structure in which the Trp strongly interacts with Pro12.  ...  Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.  ...  We also thank Vanessa Leone, Paolo Carloni, Rolando Hong and Xevi Biarnes for useful discussions and for reading the manuscript before submission. Author Contributions  ... 
doi:10.1371/journal.pcbi.1000452 pmid:19662155 pmcid:PMC2711228 fatcat:5bekmgc27vf6jjloykrhufbkvi
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