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Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives

Petras J Kundrotas, Emil G Alexov
2006 BMC Bioinformatics  
The correlated mutations (CM) method serves as the most promising approach and it has been used to predict amino acids pairs that are distant in the primary sequence but form contacts in the native 3D  ...  Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the predicted 3D structures.  ...  Acknowledgements The authors thank Barry Honig for his continuous support. The technical help of Amber Allardice is appreciated.  ... 
doi:10.1186/1471-2105-7-503 pmid:17109752 pmcid:PMC1654194 fatcat:c7xcreo235c27jpnv6lescgzfi

Two strategies to engineer flexible loops for improved enzyme thermostability

Haoran Yu, Yihan Yan, Cheng Zhang, Paul A. Dalby
2017 Scientific Reports  
Both of the two strategies investigated were useful in guiding mutation candidates to flexible loops, and had the potential to be used for other enzymes.  ...  Based on a statistical analysis of the stability changes for all variants, the qualitative prediction accuracy of the Rosetta program reached 65.3%.  ...  Acknowledgements We thank the Chinese Scholarship Council (stipend to H. Y.) for financial support. Author Contributions  ... 
doi:10.1038/srep41212 pmid:28145457 pmcid:PMC5286519 fatcat:s5q4por4mrhg7cpv5w5nwqgss4

ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses

J. Binkley, K. Karra, A. Kirby, M. Hosobuchi, E. A. Stone, A. Sidow
2009 Genome Research  
We then tabulated frequencies of true-positive, true-negative, false-positive, and false-negative predictions, and used them to produce ROC plots (Fig. 5A -E; Hanley and McNeil 1982) .  ...  For the full range of rate value thresholds of constraint prediction, the true-positive rate (TP/[TP + FN]) is plotted along the vertical axis against the false-positive rate (FP/[FP + TN]) on the horizontal  ... 
doi:10.1101/gr.097121.109 pmid:19846609 pmcid:PMC2798826 fatcat:efideknhb5fs7p2rt5jrdvfgqm

Docking and chemoinformatic screens for new ligands and targets

Peter Kolb, Rafaela S Ferreira, John J Irwin, Brian K Shoichet
2009 Current Opinion in Biotechnology  
Increasingly, the hit rates, the true-positives, and the false-positives from the docking screens are being compared to those from empirical, high-throughput screens, revealing the strengths, weaknesses  ...  This method, which returns to an older, pharmacology logic, has been surprisingly successful in predicting new 'offtargets' for established drugs.  ...  Several key interacting residues are marked. Red and green dashed lines indicate polar and hydrophobic contacts, respectively.  ... 
doi:10.1016/j.copbio.2009.08.003 pmid:19733475 pmcid:PMC2766606 fatcat:eabfhmlafbezvglpxwf5u6u57y

Mapping Causal Variants with Single-Nucleotide Resolution Reveals Biochemical Drivers of Phenotypic Change

Richard She, Daniel F. Jarosz
2018 Cell  
This 'super-resolution' approach allowed us to map 370 causal variants across 26 quantitative traits.  ...  Missense, synonymous, and cis-regulatory mutations collectively gave rise to phenotypic diversity, providing mechanistic insight into the basis of evolutionary divergence.  ...  Independent predictions were run for amino acid sequences containing either the wine or clinical variant at the causal position. Disordered residues were defined using DISOPRED3.  ... 
doi:10.1016/j.cell.2017.12.015 pmid:29373829 pmcid:PMC5788306 fatcat:23ixx76nzndixhoqqh5dd5jjs4

Alternative (non-animal) methods for cosmetics testing: current status and future prospects—2010

Sarah Adler, David Basketter, Stuart Creton, Olavi Pelkonen, Jan van Benthem, Valérie Zuang, Klaus Ejner Andersen, Alexandre Angers-Loustau, Aynur Aptula, Anna Bal-Price, Emilio Benfenati, Ulrike Bernauer (+43 others)
2011 Archives of Toxicology  
Disclaimer: This report represents the opinions of the authors as individual scientists, and should not be taken to represent the positions of any institutions, including those of ECVAM and the other Services  ...  The selected experts were asked to analyse the status and prospects of alternative methods and to provide a scientifically sound estimate of the time necessary to achieve full replacement of animal testing  ...  The model is reported to have a high positive predictivity and a low false positive rate, implying that it could be used to identify toxic chemicals.  ... 
doi:10.1007/s00204-011-0693-2 pmid:21533817 fatcat:7wqut2zliraqjfoxrrdjryei5e

Homology models of mouse and rat estrogen receptor-α ligand-binding domain created by in silico mutagenesis of a human template: Molecular docking with 17β-estradiol, diethylstilbestrol, and paraben analogs

Thomas L. Gonzalez, James M. Rae, Justin A. Colacino, Rudy J. Richardson
2019 Computational Toxicology  
Likewise, numbers of interspecies ligand-receptor residue contacts were highly correlated: Pearson r = 0.913 (human-mouse) and 0.925 (human-rat).  ...  To test this hypothesis, we used the human ERα-LBD structure (PDB 3UUD) as a template to produce rat and mouse homology models.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.  ... 
doi:10.1016/j.comtox.2018.11.003 pmid:30740556 pmcid:PMC6363358 fatcat:7o4o5lnadfgr5k2f2rbzrz6hl4

Motivations and Methods for Analyzing Pulsatile Hormone Secretion

Johannes D. Veldhuis, Daniel M. Keenan, Steven M. Pincus
2008 Endocrine reviews  
Failure of the target organ IV. Early Methods of Pulse Analysis A. Empirical threshold approaches B. Semiempirical baseline strategies V. Criteria for Optimal Pulse Analysis VI.  ...  Fixed half-life deconvolution methods D. Challenges in deconvolution analysis E. Simplifying assumptions in deconvolution analysis F. Impact of analytical assumptions on secretion estimates G.  ...  This work was supported in part via the Clinical-Translational Research-Center Grant MO1 RR00585 to the Mayo Clinic and Foundation from the National Center for Research Resources (Rockville, MD), and by  ... 
doi:10.1210/er.2008-0005 pmid:18940916 pmcid:PMC2647703 fatcat:nfh3m7x64ne25ojtyyv77zg3zu

Vol. 1, No. 2 (Full Issue)

2002 Journal of Modern Applied Statistical Methods  
The empirical basis is fallible, and yet the method of conjectures and refutations is untouched by Hume's insights.  ...  The implications for statistical methodology is that the requisite severity of testing is achieved through the use of robust procedures, whose assumptions have not been shown to be substantially violated  ...  point in time) are exchangeable as are the residuals from a model incorporating serial correlation.  ... 
doi:10.22237/jmasm/1036110660 fatcat:fprcbff3cbafzgoubiyiczlxdm

Protein Structural Alignments From Sequence [article]

Jamie Morton, Charlie Strauss, Robert Blackwell, Daniel Berenberg, Vladimir Gligorijevic, Richard Bonneau
2020 bioRxiv   pre-print
Recent work suggests that using machine learning language models can improve remote homology detection.  ...  Computing sequence similarity is a fundamental task in biology, with alignment forming the basis for the annotation of genes and genomes and providing the core data structures for evolutionary analysis  ...  Acknowledgements We would like to thank Ian Fisk and Nick Carriero for providing the computer support required to train these models.  ... 
doi:10.1101/2020.11.03.365932 fatcat:eagutucrqjhxfa3xsucsxq6g3y

Protein kinases display minimal interpositional dependence on substrate sequence: potential implications for the evolution of signalling networks

B. A. Joughin, C. Liu, D. A. Lauffenburger, C. W. V. Hogue, M. B. Yaffe
2012 Philosophical Transactions of the Royal Society of London. Biological Sciences  
We used data from experiments on the kinases ATM/ATR and CDK1, and curated CK2 substrates to evaluate the prevalence of interactions between substrate positions within a motif and the utility of these  ...  Significant increases in the ability of models to predict kinase -substrate specificity beyond position-independent models must come largely from inclusion of elements of biological and cellular context  ...  The authors thank members of their research groups, and particularly Dr David Clarke for helpful discussion.  ... 
doi:10.1098/rstb.2012.0010 pmid:22889908 pmcid:PMC3415838 fatcat:aj2qt7easzcvbo6ehzcucxkmr4

Deep Learning for Genomics: A Concise Overview [article]

Tianwei Yue, Haohan Wang
2018 arXiv   pre-print
This data explosion is constantly challenging conventional methods used in genomics.  ...  In parallel with the urgent demand for robust algorithms, deep learning has succeeded in a variety of fields such as vision, speech, and text processing.  ...  Acknowledgments We would like to acknowledge the inspiration from a course instructed by Kundaje and Zou (2016) , and two reviews contributed by Min et al. (2017) and Ching et al. (2017) 8 . 8.  ... 
arXiv:1802.00810v2 fatcat:u6s7pz2p6jdxzodz5k34it2hiu

Detection of HIV transmission hotspots in British Columbia, Canada: A novel framework for the prioritization and allocation of treatment and prevention resources

Angela McLaughlin, Paul Sereda, Natalia Oliveira, Rolando Barrios, Chanson J. Brumme, Zabrina L. Brumme, Julio S.G. Montaner, Jeffrey B. Joy
2019 EBioMedicine  
In a blind prediction of 2018 cases, diversification rate improved the model's specificity by 12%, accuracy by 9%, top 20 agreement by 100%, and correlation of predicted and observed values by 162% relative  ...  The predictive power of the model was compared with a phylogenetically uninformed model.  ...  All inferences, opinions, and conclusions drawn in this paper are those of the authors, and do not reflect the opinions of the funders. Supplementary material  ... 
doi:10.1016/j.ebiom.2019.09.026 pmid:31628022 pmcid:PMC6838403 fatcat:pezkyulqkvcavnq5t3rqxzxoje

Which criteria should we use to end isolation in hemodialysis patients with COVID-19?

Gaetano Alfano, Francesco Fontana, Annachiara Ferrari, Niccolò Morisi, Mariacristina Gregorini, Gianni Cappelli, Riccardo Magistroni, Giovanni Guaraldi, Gabriele Donati
2022 Clinical Kidney Journal  
Recent results seem to encourage the use of RT-PCR cycle threshold (Ct) values and antigenic tests given their better correlation with cell culture for SARS-CoV-2 than RT-PCR testing.  ...  pragmatic procedure to end isolation in COVID-19 patients on HD.  ...  ACKNOWLEDGEMENTS Special thanks are due to nephrologists (Fabio Olmeda, Salvatore Perrone, Lucia Stipo) and the dialysis nurses who have faced COVID-19 outbreaks at the Dialysis Unit of Modena.  ... 
doi:10.1093/ckj/sfac115 fatcat:vxn62kam25dhni22qb7bwtujoi

An Approach to Understanding the Transmission of Mycobacterium leprae Using Molecular and Immunological Methods: Results from the MILEP2 Study

W. Cairns S. Smith, Christine M. Smith, Ian A. Cree, Ruprendra S. Jadhav, Murdo Macdonald, Vijay K. Edward, Linda Oskam, Stella van Beers, Paul Klatser
2004 International journal of leprosy and other mycobacterial diseases  
This gives a fairly low false positivity rate of 8.6%, but a false negative rate of 14.7%. The positive predictive value is 39.5% and the negative predictive value is 98.9% (Table 4) .  ...  The constraints lie in the distinct possibility of false positive results due to external contamination and in the lack of structural correlation, both of which are obviated with use of in situ procedures  ...  There are no ready pragmatic methods to monitor the progress of leprosy elimination programs. We therefore tried to explore newer methods to answer these demands.  ... 
doi:10.1489/0020-7349(2004)72<269:aatutt>2.0.co;2 pmid:15485283 fatcat:goelml5hfjbmdee5lpzvwxdxhq
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