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EXPLORING BIAS IN THE PROTEIN DATA BANK USING CONTRAST CLASSIFIERS

K. PENG, Z. OBRADOVIC, S. VUCETIC
2003 Biocomputing 2004  
In this study we analyzed the bias existing in the Protein Data Bank (PDB) using the novel contrast classifier approach.  ...  We applied the contrast classifier to SWISS-PROT sequences to analyze the bias in PDB towards different functional protein properties.  ...  We applied the contrast classifier to explore the bias existing in the Protein Data Bank towards different functional protein properties.  ... 
doi:10.1142/9789812704856_0041 fatcat:7zpi24euibedrpav5miu75xj2q

Exploring bias in the Protein Data Bank using contrast classifiers

K Peng, Z Obradovic, S Vucetic
2004 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
In this study we analyzed the bias existing in the Protein Data Bank (PDB) using the novel contrast classifier approach.  ...  We applied the contrast classifier to SWISS-PROT sequences to analyze the bias in PDB towards different functional protein properties.  ...  We applied the contrast classifier to explore the bias existing in the Protein Data Bank towards different functional protein properties.  ... 
pmid:14992523 fatcat:yohtc7u4djci7d6kwtyg43dlay

Serum C-reactive protein, procalcitonin, and lactate dehydrogenase for the diagnosis of pancreatic necrosis

Oluyemi Komolafe, Stephen P Pereira, Brian R Davidson, Kurinchi Selvan Gurusamy
2017 The Cochrane library  
Overall, none of the tests assessed in this review were sufficiently accurate to suggest that they could be useful in clinical practice.  ...  Key results Variations in when the studies carried out the blood tests and what level was considered abnormal meant that we were unable to combine the data to provide the overall results.  ...  as at high risk of bias as they all used CECT or surgery as the reference standard and were therefore classified as 'no' for the question "Is the reference standard likely to correctly classify the target  ... 
doi:10.1002/14651858.cd012645 pmid:28431197 fatcat:eyumzv2kqjanjmc7cqrrcl243i

Structural Dynamics is a Determinant of the Functional Significance of Missense Variants

Luca Ponzoni, Ivet Bahar
2018 Biophysical Journal  
Two major types of data are used to this aim: sequence conservation/ evolution and structural properties.  ...  Our study suggests that the class of dynamics descriptors introduced here may be used in conjunction with existing features to not only increase the prediction accuracy of the impact of variants on biological  ...  We acknowledge useful discussions with Dr. David Whitcomb on CFTR variants and with Dr. Sean Mooney on PolyPhen-2.  ... 
doi:10.1016/j.bpj.2017.11.1291 fatcat:x7v4nnco5jbitglocswsy4btee

Dynamic transcriptome of mice

Yoshihide Hayashizaki, Mutsumi Kanamori
2004 Trends in Biotechnology  
This work was mainly supported by research grants for the RIKEN Genome Exploration Research project and the National Project on Protein Structural and Functional Analysis from MEXT of the Japanese government  ...  Acknowledgements We thank all the members of the RIKEN Genome Research Exploration Group and Genome Science Laboratory and the FANTOM consortium for their devoted contributions.  ...  In this protocol, we did not use the polymerase chain reaction (PCR) because this produces a large cloning bias.  ... 
doi:10.1016/j.tibtech.2004.02.003 pmid:15038920 fatcat:5jsr2i4fabfztl4douezvgpgfi

Bioinformatics approaches for improved recombinant protein production in Escherichia coli: protein solubility prediction

C. C. H. Chang, J. Song, B. T. Tey, R. N. Ramanan
2013 Briefings in Bioinformatics  
evaluation conducted and reported in different literature [8] , by setting the threshold value for soluble class at 50 and using training data set as the independent test data set. n/a, not applicable  ...  In this article, we review and compare seven prediction tools available, which predict the solubility of protein expressed in E. coli, using the following criteria: prediction performance, usability, utility  ...  Acknowledgements The authors are grateful to Monash University Sunway Campus Malaysia for providing the research support needed for this work.  ... 
doi:10.1093/bib/bbt057 pmid:23926206 fatcat:c6za7l2rejbyhepzpvzbfcbdgq

An ImmunoSignature test distinguishes Trypanosoma cruzi, hepatitis B, hepatitis C and West Nile virus seropositivity among asymptomatic blood donors

Michael Rowe, Jonathan Melnick, Robert Gerwien, Joseph B. Legutki, Jessica Pfeilsticker, Theodore M. Tarasow, Kathryn F. Sykes, Barbara A. Burleigh
2017 PLoS Neglected Tropical Diseases  
Its potential contribution for monitoring and controlling Chagas lies in IST's delivery of higher resolution immune-state readouts than obtained with currently-used technologies.  ...  Author summary The most prevalent parasite infection in Latin America causes Chagas' disease.  ...  Acknowledgments The authors would like to acknowledge and thank David Lomeli and Kathryn Nielsen for their work in conducting the assays, Scott Melville and Glenn Hein for designing sample layouts  ... 
doi:10.1371/journal.pntd.0005882 pmid:28873423 pmcid:PMC5600393 fatcat:huo56qgtmbaclnj5bijl54vlpq

Structural dynamics is a determinant of the functional significance of missense variants

Luca Ponzoni, Ivet Bahar
2018 Proceedings of the National Academy of Sciences of the United States of America  
We acknowledge useful discussions with Dr. David Whitcomb on CFTR variants and with Dr. Sean Mooney on PolyPhen-2.  ...  The authors declare no conflict of interest. This article is a PNAS Direct Submission. R.L.J. is a guest editor invited by the Editorial Board. ACKNOWLEDGMENTS.  ...  Currently (February 2018), there are more than 6,300 UniProt Knowledgbase entries out of 71,772 proteins reported in the Homo sapiens proteome that have structural data in the Protein Data Bank (PDB).  ... 
doi:10.1073/pnas.1715896115 pmid:29610305 pmcid:PMC5910821 fatcat:2tyhcd5pl5dgbls4vxelv6arty

RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence

Wen-Jun Shen, Wenjuan Cui, Danze Chen, Jieming Zhang, Jianzhen Xu
2018 Molecules  
For the RPiRLS classifier, each protein sequence comprises up to 20 diverse amino acids but for the RPiRLS-7G classifier, each protein sequence is represented by using 7-letter reduced alphabets based  ...  As the number of available RNA-protein binding experimental data has increased rapidly due to high-throughput sequencing methods, it is now possible to measure and understand RNA-protein interactions by  ...  Materials and Methods Training Data Set The increase of the number of protein-RNA complexes in Protein Data Bank [47] has opened possibilities for researchers to develop secondary data bases and to  ... 
doi:10.3390/molecules23030540 pmid:29495575 fatcat:htngwy4ti5fwloolvxuoi3lji4

Prediction of protein crystallization using collocation of amino acid pairs

Ke Chen, Lukasz Kurgan, Mandana Rahbari
2007 Biochemical and Biophysical Research Communications - BBRC  
While above 80% of protein structures in PDB were determined using X-ray crystallography, in some cases only 42% of soluble purified proteins yield crystals.  ...  Frishman, Will my protein crystallize? A sequence-based predictor, Proteins 62 (2) (2006) [343][344][345][346][347][348][349][350][351][352][353][354][355], and other state-of-the-art classifiers.  ...  Acknowledgment This research was supported in part by the Natural Sciences and Engineering Research Council of Canada under the Discovery program.  ... 
doi:10.1016/j.bbrc.2007.02.040 pmid:17316561 fatcat:ab54wis2uvemnaap3kbx5qlkue

Unexpected features of the dark proteome

Nelson Perdigão, Julian Heinrich, Christian Stolte, Kenneth S. Sabir, Michael J. Buckley, Bruce Tabor, Beth Signal, Brian S. Gloss, Christopher J. Hammang, Burkhard Rost, Andrea Schafferhans, Seán I. O'Donoghue
2015 Proceedings of the National Academy of Sciences of the United States of America  
Data Bank (PDB) (1) of experimentally determined macromolecular structures recently surpassed 110,000 entries-a landmark in understanding the molecular machinery of life.  ...  Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure.  ...  as the Alexander von Humboldt Foundation, and the Fundação para a Ciência e Tecnologia.  ... 
doi:10.1073/pnas.1508380112 pmid:26578815 pmcid:PMC4702990 fatcat:u6kfcwbrwfasfj7polmlilavv4

Deep Learning for Validating and Estimating Resolution of Cryo-Electron Microscopy Density Maps †

Todor Avramov, Dan Vyenielo, Josue Gomez-Blanco, Swathi Adinarayanan, Javier Vargas, Dong Si
2019 Molecules  
In this study, we first propose supervised deep learning methods to extract representative 3D features at high, medium and low resolutions from simulated protein density maps and build classification models  ...  The trained models can classify a given 3D cryo-EM density map into one of three resolution levels: high, medium, low.  ...  Acknowledgments: We gratefully acknowledge the support of NVIDIA Corporation (Santa Clara, CA, USA) with the donation of the GPU used for this research.  ... 
doi:10.3390/molecules24061181 fatcat:y5zhn2lk6fchtj3rms7mx2tmr4

Exploring machine learning: A bibliometric general approach using SciMAT

Juan Rincon-Patino, Gustavo Ramirez-Gonzalez, Juan Carlos Corrales
2018 F1000Research  
be the basis for future developments in the field.  ...  research field in the future.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.12688/f1000research.15620.1 fatcat:q7h335tlrfdujl3d4uwtirehta

RPI-SE: a stacking ensemble learning framework for ncRNA-protein interactions prediction using sequence information

Hai-Cheng Yi, Zhu-Hong You, Mei-Neng Wang, Zhen-Hao Guo, Yan-Bin Wang, Ji-Ren Zhou
2020 BMC Bioinformatics  
Finally, an ensemble learning framework integrated different types of base classifier is developed to predict ncRNA-protein interactions using these discriminative features.  ...  The interactions between non-coding RNAs (ncRNA) and proteins play an essential role in many biological processes.  ...  Acknowledgements The authors would like to thank all the editors and anonymous reviewers for their constructive advices.  ... 
doi:10.1186/s12859-020-3406-0 pmid:32070279 fatcat:ktw7rqqnvfb4pjyjedl5ryj3mm

NOTCH1, HIF1A and Other Cancer-Related Proteins in Lung Tissue from Uranium Miners—Variation by Occupational Exposure and Subtype of Lung Cancer

Beate Pesch, Swaantje Casjens, Ingo Stricker, Daniela Westerwick, Dirk Taeger, Sylvia Rabstein, Thorsten Wiethege, Andrea Tannapfel, Thomas Brüning, Georg Johnen, Ramon Andrade de Mello
2012 PLoS ONE  
Moreover, we investigated whether these cancerrelated proteins can classify lung cancer using supervised and unsupervised classification.  ...  We investigated the association of cumulative exposure to these carcinogens with NOTCH1, HIF1A and other cancer-specific proteins in lung tissue from uranium miners.  ...  Acknowledgments The authors thank Johannes Gellissen, Federal Institute for Occupational Safety and Health, and the team of the Health Data Archive of the WISMUT corporation for retrieving smoking data  ... 
doi:10.1371/journal.pone.0045305 pmid:23028920 pmcid:PMC3444449 fatcat:wn3agusccba4xnf3ou24pxsnou
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