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EXPLORING BIAS IN THE PROTEIN DATA BANK USING CONTRAST CLASSIFIERS
2003
Biocomputing 2004
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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
2004
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
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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
2017
The Cochrane library
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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
2018
Biophysical Journal
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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
2004
Trends in Biotechnology
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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
2013
Briefings in Bioinformatics
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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
2017
PLoS Neglected Tropical Diseases
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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
2018
Proceedings of the National Academy of Sciences of the United States of America
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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
2018
Molecules
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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
2007
Biochemical and Biophysical Research Communications - BBRC
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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
2015
Proceedings of the National Academy of Sciences of the United States of America
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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 †
2019
Molecules
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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
2018
F1000Research
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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
2020
BMC Bioinformatics
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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
2012
PLoS ONE
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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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