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A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains

K. Kundu, F. Costa, R. Backofen
2013 Bioinformatics  
Results: Here, we present a machine-learning approach based on an efficient graph-kernel technique to predict the specificity of a large set of 70 human SH3 domains, which are an important class of PRMs  ...  We also provide a genome-wide prediction for all 70 human SH3 domains, which can be found under  ...  ACKNOWLEDGEMENTS The authors thank David Gfeller and TaeHyung Kim for their help with the MUSI tool.  ... 
doi:10.1093/bioinformatics/btt220 pmid:23813002 pmcid:PMC3694653 fatcat:qskdmbnbdbf5dendwftxzqm4ii

Optimizing the Amino Acid Sequences of Peptides and Improving Their Specificity of Binding to SH3 Domains of Target Proteins

Yanrong Ren, Qiang Wang, Xiaobo Li
2017 Indian Journal of Pharmaceutical Education and Research  
It is always a crucial challenge in biotechnology to avoid promiscuous binding between an anticancer peptide and multiple SH3 domains, thus reducing potential toxic effects.  ...  of binding to the SH3 domain of c-Src protein.  ...  SH3PepInt was a tool provided by MoDPepInt, 26 which used graph kernel approach to perform alignment-free prediction of domain-peptide interaction.  ... 
doi:10.5530/ijper.51.1.7 fatcat:5cj323gruzh4lb5e2yvxdacc3y

Classification of signaling proteins based on molecular star graph descriptors using Machine Learning models

Carlos Fernandez-Lozano, Rubén F. Cuiñas, José A. Seoane, Enrique Fernández-Blanco, Julian Dorado, Cristian R. Munteanu
2015 Journal of Theoretical Biology  
) technique with the Laplacian kernel (RFE-LAP) and an AUROC of 0.961.  ...  Important signaling pathways are presented for three UniprotIDs (34 PDBs) with a signaling prediction greater than 98.0%.  ...  The authors would like to thank the Galician Supercomputing Centre (CESGA) for the provision of computational support and acknowledge the support from the Galician Network of Drugs R+D REGID (Xunta de  ... 
doi:10.1016/j.jtbi.2015.07.038 pmid:26297890 fatcat:baktblpytvgvla6bsdxrloai2m

Programme Booklet Of The 11Th Iscb Student Council Symposium, Dublin, 2015 [article]

Mehedi Hassan, R Gonzalo Parra
2015 Zenodo  
This is a booklet containing programme of the day of the 11th ISCB Student Council Symposium, Dublin, 10 July 2015. This also contains all the abstracts of works presented on the day.  ...  For instance, SH3 domains bind preferably to proline-rich aminoacid motifs.  ...  Our results provide novel insights suggesting that the Fyn SH3 domain must contain different signatures of amino acids to promote binding to various peptide classes.  ... 
doi:10.5281/zenodo.1253018 fatcat:b75h2xdwmralzfqdhs6jd6k4vm

Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

Domenico Fraccalvieri, Alessandro Pandini, Fabio Stella, Laura Bonati
2011 BMC Bioinformatics  
The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time.  ...  We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering.  ...  Then we present the application of the proposed two-level approach, with the optimized parameters, to the conformational and functional analysis of a test case composed of the α-spectrin SH3 (Spc-SH3)  ... 
doi:10.1186/1471-2105-12-158 pmid:21569575 pmcid:PMC3118354 fatcat:xmw6mfrvarglxdxqoe4nibammq

Award Winners and Abstracts of the 30th Anniversary Symposium of The Protein Society, Baltimore, MD, July 16-19, 2016

2016 Protein Science  
In light of the structure we provide a putative explanation for the greatly compromised physiological activity as well as for the enhanced ROS-generation.  ...  The D444V pathogenic amino acid substitution of human (h) E3 leads to hypotonia, microcephaly, lactic acidosis, developmental delay, and hypoglycemia.  ...  The goal is to provide a validated approach to functional annotation for wider application by the community.  ... 
doi:10.1002/pro.3026 pmid:27783432 pmcid:PMC5081090 fatcat:c4k7luvl4vczfpol76ycqo4nji

Data- and knowledge-based modeling of gene regulatory networks: an update

Jörg Linde, Sylvie Schulze, Sebastian G Henkel, Reinhard Guthke
2015 EXCLI Journal : Experimental and Clinical Sciences  
Gene regulatory network inference is a systems biology approach which predicts interactions between genes with the help of high-throughput data.  ...  After the advance of Next-Generation-Sequencing of cDNAs derived from RNA samples (RNA-Seq) we discuss in detail its application to network inference.  ...  Acknowledgements This work was supported by the Deutsche Forschungsgemeinschaft (DFG) CRC/Transregio 124 'Pathogenic fungi and their human host: Networks of interaction', subproject INF (JL, RG) and B3  ... 
doi:10.17179/excli2015-168 pmid:27047314 pmcid:PMC4817425 fatcat:lebwxkplx5grrmffprjupt4poi

Prediction of Protein Subcellular Localization Based on Primary Sequence Data [chapter]

Mert Özarar, Volkan Atalay, Rengül Çetin Atalay
2003 Lecture Notes in Computer Science  
The approach for prediction is to find the most frequent motifs for each protein in a given class based on clustering via self organizing maps and then to use these most frequent motifs as features for  ...  This approach allows a classification independent of the length of the sequence.  ...  It may be a novel work designed for human only. For realizing this, SWISS PROT should be re-parsed to separate human genes.  ... 
doi:10.1007/978-3-540-39737-3_76 fatcat:2b2jcni5tjemralp2sdfhqyrcu

BioCreative II Workshop Proceedings

Lynette, Martin, Alfonso
2007 Zenodo  
Entity Recognition with Combinations of Conditional Random Fields 93 Gene Mention Recognition Using Lexicon Match Based Two-Layer Support Vector Machines 97 Using Semi-Supervised Techniques to Detect  ...  community with high quality molecular interaction data 69 IASL Systems in the Gene Mention Tagging Task and Protein Interaction Article Sub-task 77 Identifying Gene Mentions by Case-Based Classifi cation  ...  Acknowledgements We would like to thank Zhiqiang Gu for his implementation of p-spectrum kernel using trie-structure, which had reduced a large amount of computation.  ... 
doi:10.5281/zenodo.4274543 fatcat:3sa3fvgngffjrblxzgswof42tq

Uncovering Aberrant Mutant PKA Function with Flow Cytometric FRET

Shin-Rong Lee, Lingjie Sang, David T. Yue
2016 Cell Reports  
We are forever indebted to our mentor, the late D.T.Y., for his leadership and for showing us how to approach science with grace and humility. This work is supported by MSTP funding (to S.  ...  We are grateful to Wanjun Yang for her assistance with cell culture and other members of the Calcium Signals Lab for insightful contributions while this work was at an early stage.  ...  With an appropriate binding model, a binding curve can then be constructed, with each cell contributing a point on the graph ( Figure 1B) .  ... 
doi:10.1016/j.celrep.2016.02.077 pmid:26997269 pmcid:PMC4814300 fatcat:ykkztwloqremvm3gvcanhhpfmq

Molecular Approaches to Safe and Controlled Engineered T-cell Therapy
Молекулярные подходы к безопасной и контролируемой Т-клеточной терапии

R. S. Kalinin, A. V. Petukhov, V. D. Knorre, M. A. Maschan, A. V. Stepanov, A.G. Gabibov
2018 Acta Naturae  
This new approach can be used in a wide spectrum of tasks that require  ...  Authors also showed that a combination of genetic Cre-eGFP labeling with immunohistochemical staining of the endog enous c-Fos protein allows one to identify and compare the neuronal populations that are  ...  This study was supported by the Russian Foundation for Basic Research as the part of scientific projects No. 18  ... 
doi:10.32607/2075851-2018-10-2-16-23 fatcat:pi6vvjaxmfchha5vwbuovmqtai

Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA [article]

Piotr Klukowski, Roland Riek, Peter Güntert
2022 arXiv   pre-print
Tested on a 100-protein benchmark comprising 1329 multidimensional NMR spectra, ARTINA demonstrated its ability to solve structures with 1.44 Å median RMSD to the PDB reference and to identify 91.36 reducing  ...  the effort for a protein assignment or structure determination by NMR essentially to the preparation of the sample and the spectra measurements.  ...  .), and a Grant-in-Aid for Scientific Research of the Japan Society for the Promotion of Science (P.G., 20 K06508).  ... 
arXiv:2201.12041v4 fatcat:jy7tcp5d6jgnvnwp2tn7izvupq

PMF (peptide-mass fingerprinting) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Using a yeast two-hybrid screen with POSH (plenty of SH3 domains, a scaffold involved in activation of the apoptotic JNK/c-Jun pathway) as the bait, identified an interaction between POSH and Nix and contributed  ...  There is a possible therapeutic approach to prostate cancer in overexpressing an androgen receptor by ligand-independent activation of the N-terminal domain peptide to create decoy molecules that competitively  ...  It is a newer alternative for the pfu units but it is supposed to be employed for highly purified preparations.  ... 
doi:10.1007/978-1-4020-6754-9_13064 fatcat:pzr5w5d5tvbyte6vp2kh3unfhe

Pelger(-Huet) Anomaly [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Using a yeast two-hybrid screen with POSH (plenty of SH3 domains, a scaffold involved in activation of the apoptotic JNK/c-Jun pathway) as the bait, identified an interaction between POSH and Nix and contributed  ...  There is a possible therapeutic approach to prostate cancer in overexpressing an androgen receptor by ligand-independent activation of the N-terminal domain peptide to create decoy molecules that competitively  ...  It is a newer alternative for the pfu units but it is supposed to be employed for highly purified preparations.  ... 
doi:10.1007/978-1-4020-6754-9_12490 fatcat:htaav6px6zcbbfuhaastehriru

Patristic Distance [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Using a yeast two-hybrid screen with POSH (plenty of SH3 domains, a scaffold involved in activation of the apoptotic JNK/c-Jun pathway) as the bait, identified an interaction between POSH and Nix and contributed  ...  There is a possible therapeutic approach to prostate cancer in overexpressing an androgen receptor by ligand-independent activation of the N-terminal domain peptide to create decoy molecules that competitively  ...  It is a newer alternative for the pfu units but it is supposed to be employed for highly purified preparations.  ... 
doi:10.1007/978-1-4020-6754-9_12406 fatcat:3qmewhcngva3tg4xf3ople4hxi
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