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Topology of functional networks predicts physical binding of proteins

Ömer Sinan Saraç, Vera Pancaldi, Jürg Bähler, Andreas Beyer
2012 Computer applications in the biosciences : CABIOS  
into different types of physical protein associations.  ...  We demonstrate the utility of network features based on human and budding yeast networks; we show that network features can distinguish different sub-types of physical protein associations and we apply  ...  Herein, we show that combining topological features with other lines of evidence improves the specificity when predicting physical protein binding from functional networks.  ... 
doi:10.1093/bioinformatics/bts351 pmid:22718785 fatcat:qyj6dzbfjvgpfkp4ouwppldwyi

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

Zixuan Cang, Guo-Wei Wei, Roland L. Dunbrack
2017 PLoS Computational Biology  
We further integrate ESPH and convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability  ...  We demonstrate that the present TopologyNet architectures outperform other state-of-the-art methods in the predictions of protein-ligand binding affinities, globular protein mutation impacts, and membrane  ...  TopologyNet for biomolecular property predictions  ... 
doi:10.1371/journal.pcbi.1005690 pmid:28749969 pmcid:PMC5549771 fatcat:ntcs3edkyreunor2lm6uamzrzu

Functional homogeneity and specificity of topological modules in human proteome

Rama Kaalia, Jagath C. Rajapakse
2019 BMC Bioinformatics  
Specifically, we determined the effects on functional homogeneity and heterogeneity of topological modules (i) with both physical and functional protein-protein interactions; and (ii) with incorporation  ...  Weighted networks result in more number of topological modules but did not affect their functional propensity.  ...  Funding This research and publications costs are supported by Tier-2 MOE2016-T2-1-029 grant by the Ministry of Education, Singapore.  ... 
doi:10.1186/s12859-018-2549-8 pmid:30717667 pmcid:PMC7394330 fatcat:h7sfvfkq5ndwdfmoemqwupjf7i

Topological fingerprints reveal protein-ligand binding mechanism [article]

Zixuan Cang, Guo-Wei Wei
2017 arXiv   pre-print
Accurate prediction of protein-ligand binding affinities is vital to rational drug design and the understanding of protein-ligand binding and binding induced function.  ...  The combination of ESPH and machine learning gives rise to one of the most efficient and powerful tools for revealing protein-ligand binding mechanism and for predicting binding affinities.  ...  Essentially, there are three types of scoring functions for protein-ligand binding predictions: physics based, 4, 5 knowledge based 6 and empirical ones.  ... 
arXiv:1703.10982v1 fatcat:xmtnh3jfmbfxjcdn7dwgqxqh6e

Evolutionary Pressure on the Topology of Protein Interface Interaction Networks

Margaret E. Johnson, Gerhard Hummer
2013 Journal of Physical Chemistry B  
The densely connected structure of protein-protein interaction (PPI) networks reflects the functional need of proteins to cooperate in cellular processes.  ...  We show that the topology of the IIN is under evolutionary pressure, and we connect topological features of the IIN to specific biological functions.  ...  Acknowledgments This work was supported by the Intramural Research Program of the NIDDK, NIH and by an NIH K99 award GM098371 to MEJ. The research used the Biowulf Linux cluster at the NIH.  ... 
doi:10.1021/jp402944e pmid:23701316 pmcid:PMC3808520 fatcat:yd3vcgg3qbagnayfpsrrmmw2vi

Drug target prioritization by perturbed gene expression and network information

Zerrin Isik, Christoph Baldow, Carlo Vittorio Cannistraci, Michael Schroeder
2015 Scientific Reports  
The term "target" can refer either to proteins physically binding to the drug or to proteins that are only functionally related.  ...  Protein-protein interaction (PPI) networks provide such down-stream relationships between targets and proteins by using physical contacts, genetic interactions and functional relationships.  ...  Joachim Haupt for sharing physical target database and very fruitful discussions, and Matthias Kuhn for statistical discussions.  ... 
doi:10.1038/srep17417 pmid:26615774 pmcid:PMC4663505 fatcat:dfjifgn6zbh3feno2sdgw426ym

Exact Identification of Topologically Essential Interactions in the Networks Derived from Perturbation Experiments

Maxim N. Artyomov, Ana Paula Leite, Aviv Regev
2011 Biophysical Journal  
Our finding indicate that different levels of SYT and CPX have computational consequences at nerve terminal that modulate basal noise, output gain, speed of transmission and the short-term plasticity.  ...  Genetic interaction and kinetics analysis reveals that CPX and SYT expression modulate the rates of spontaneous and synchronous/ asynchronous release.  ...  We demonstrate how the scaling of this power law depends on the size of the binding interfaces and the topology of the protein interaction network.  ... 
doi:10.1016/j.bpj.2010.12.379 fatcat:g3cfwnxbibhudm4lirv6jkekqa

Prediction of protein-binding areas by small-world residue networks and application to docking

Carles Pons, Fabian Glaser, Juan Fernandez-Recio
2011 BMC Bioinformatics  
Conclusions: The network-based representation of protein structures can be used to identify protein-protein binding regions and to efficiently score docking poses, complementing energy-based approaches  ...  From such networks, it is possible to calculate different topology-based values for each of the nodes, and to identify protein regions with high centrality scores, which are known to positively correlate  ...  Interestingly, the correlation between the results obtained by these two different types of scoring functions (physics-based pyDock and topology-based network) was very low (below 0.15 for all network  ... 
doi:10.1186/1471-2105-12-378 pmid:21943333 pmcid:PMC3189935 fatcat:gpcvferlprawlnak6i2i7p4lx4

Multimodal Pre-Training Model for Sequence-based Prediction of Protein-Protein Interaction [article]

Yang Xue, Zijing Liu, Xiaomin Fang, Fan Wang
2021 arXiv   pre-print
Protein-protein interactions (PPIs) are essentials for many biological processes where two or more proteins physically bind together to achieve their functions.  ...  prediction for SARS-CoV-2, and mutation-driven binding affinity change prediction.  ...  A topology-based network tree for the prediction of proteinprotein binding affinity changes following mutation.  ... 
arXiv:2112.04814v1 fatcat:areao63ioncdrf46jr5ty6kdb4

Detection of Predictive Dynamics of Glucocorticoid Receptors in Xenopus Laevis Embryonic Tissues

YongTae Kim, Sagar D. Joshi, Philip R. LeDuc, Lance A. Davidson, William C. Messner
2011 Biophysical Journal  
Our finding indicate that different levels of SYT and CPX have computational consequences at nerve terminal that modulate basal noise, output gain, speed of transmission and the short-term plasticity.  ...  Genetic interaction and kinetics analysis reveals that CPX and SYT expression modulate the rates of spontaneous and synchronous/ asynchronous release.  ...  We demonstrate how the scaling of this power law depends on the size of the binding interfaces and the topology of the protein interaction network.  ... 
doi:10.1016/j.bpj.2010.12.380 fatcat:mqfmp3zctbhexnmtrrat75zehy

Nonspecific Binding Limits the Number of Proteins in a Cell and Shapes their Interaction Networks

Margaret E. Johnson, Gerhard Hummer
2011 Biophysical Journal  
Our finding indicate that different levels of SYT and CPX have computational consequences at nerve terminal that modulate basal noise, output gain, speed of transmission and the short-term plasticity.  ...  Genetic interaction and kinetics analysis reveals that CPX and SYT expression modulate the rates of spontaneous and synchronous/ asynchronous release.  ...  We demonstrate how the scaling of this power law depends on the size of the binding interfaces and the topology of the protein interaction network.  ... 
doi:10.1016/j.bpj.2010.12.378 fatcat:tcxn4xbwurgstniccq5ddkeway

Pattern recognition tools for proteomics

Virginio Cantoni
2014 The European Physical Journal Plus  
Protein structure analysis and comparison are important to understand the evolutionary relationships among proteins, predicting protein folding and protein functions.  ...  The identification of protein-binding sites, their classification and analysis are of interest for drug design and treatment of diseases.  ...  Protein structure analysis and comparison are important to understand the evolutionary relationships among proteins, predicting protein folding and protein functions.  ... 
doi:10.1140/epjp/i2014-14130-3 fatcat:sddaw3sbo5eb7mkkib6o23hpge

Construct and Simulate Virtual Cell with Minimum Genome at the Nanoscale

Yu Xu, Ruth Nussionv, Buyong Ma
2011 Biophysical Journal  
Our finding indicate that different levels of SYT and CPX have computational consequences at nerve terminal that modulate basal noise, output gain, speed of transmission and the short-term plasticity.  ...  Genetic interaction and kinetics analysis reveals that CPX and SYT expression modulate the rates of spontaneous and synchronous/ asynchronous release.  ...  We demonstrate how the scaling of this power law depends on the size of the binding interfaces and the topology of the protein interaction network.  ... 
doi:10.1016/j.bpj.2010.12.376 fatcat:6kqsbdprmzflziloauwignchke

Toward a Whole Cell Model of Mycoplasma Genitalium

Jonathan R. Karr, Jayodita C. Sanghvi, Jared M. Jacobs, Markus W. Covert
2011 Biophysical Journal  
Our finding indicate that different levels of SYT and CPX have computational consequences at nerve terminal that modulate basal noise, output gain, speed of transmission and the short-term plasticity.  ...  Genetic interaction and kinetics analysis reveals that CPX and SYT expression modulate the rates of spontaneous and synchronous/ asynchronous release.  ...  We demonstrate how the scaling of this power law depends on the size of the binding interfaces and the topology of the protein interaction network.  ... 
doi:10.1016/j.bpj.2010.12.377 fatcat:4lyn6jmqz5empgrwqzggwez624

Identification of putative drug targets for human sperm-egg interaction defect using protein network approach

Soudabeh Sabetian, Mohd Shahir Shamsir
2015 BMC Systems Biology  
Through topological analysis of the network with calculation of some metrics, such as connectivity and betweenness centrality, we have identified 13 essential proteins as putative drug targets.  ...  The essential proteins or potential drug targets were found using topological analysis of the protein network. These putative targets are promising for further experimental validation.  ...  Because of the networked nature of protein function, topological analysis of the protein network may help to identify essential proteins that can be potentially drug targets.  ... 
doi:10.1186/s12918-015-0186-7 pmid:26187737 pmcid:PMC4506605 fatcat:dovycj4kd5efjexdth76olbmue
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