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Predict-2nd: a tool for generalized protein local structure prediction

Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, Kevin Karplus
2008 Computer applications in the biosciences : CABIOS  
In addition, local structure predictions can be used as a component of cost functions in genetic algorithms that predict protein tertiary structure.  ...  MOTIVATION: Predictions of protein local structure, derived from sequence alignment information alone, provide visualization tools for biologists to evaluate the importance of amino acid residue positions  ...  Author contributions were Katzman: implemented guide sequences in PREDICT-2ND, Barrett: implemented early version of PREDICT-2ND, Karchin: developed testing protocol and tested many alphabets, Thiltgen  ... 
doi:10.1093/bioinformatics/btn438 pmid:18757875 pmcid:PMC2732275 fatcat:pe6kvhev7bhw7pqld3crgb4tei

Online Programs and Databases of Peptides and Proteolytic Enzymes – A Brief Update for 2007–2008

Piotr Minkiewicz, Małgorzata Darewicz, Anna Iwaniak, Justyna Michalska, Jerzy Dziuba
2009 Food Technology and Biotechnology  
, prediction of peptide structure, the occurrence of posttranslational glycosylation and immunogenicity, as well as the support of peptide design process.  ...  This paper provides a brief review of bioactive peptide databases and sequence alignment programs enabling the search for peptide motifs, determination of physicochemical properties of amino acid residues  ...  Karplus, PREDICT-2ND: A tool for generalized protein local structure prediction, Bioinformatics, 24 (2008) 2453-2459. 38. R. Gautier, D. Douguet, B. Antonny, G.  ... 
doaj:8118242caab449e9ba59273644952ea7 fatcat:x5q2oam72jhvxe4ysnxi3svica

Identification of prokaryotic small proteins using a comparative genomic approach

Josue Samayoa, Fitnat H. Yildiz, Kevin Karplus
2011 Computer applications in the biosciences : CABIOS  
Our method incorporates neural-net predictions for 3 local structure alphabets within a comparative genomic approach to generate predictions for whether or not a given open reading frame encodes for a  ...  Given this assumption, it follows that small proteins should display conserved local protein structure properties much like larger proteins.  ...  Local structure predictions All local structure predictions were generated using Predict-2nd [10] , using the amino-acid multiple alignments derived from the original DNA multiple alignment as inputs.  ... 
doi:10.1093/bioinformatics/btr275 pmid:21551138 pmcid:PMC3117347 fatcat:4csffghvlzhxdbvp2iwxtgpxua

Combining local-structure, fold-recognition, and new fold methods for protein structure prediction

Kevin Karplus, Rachel Karchin, Jenny Draper, Jonathan Casper, Yael Mandel-Gutfreund, Mark Diekhans, Richard Hughey
2003 Proteins: Structure, Function, and Bioinformatics  
This paper presents an overview of the SAM-T02 method for protein fold recognition and the undertaker program for ab initio predictions.  ...  The two-track hmms use an amino-acid alphabet and one of several different local-structure alphabets.  ...  Acknowledgments This work was supported in part by NSF grants DBI-9808007 and EIA-9905322, DOE grant DE-FG0395-99ER62849, and a National Physical Sciences Consortium graduate fellowship.  ... 
doi:10.1002/prot.10540 pmid:14579338 fatcat:2hehpi5dyvfaxa3gdmhzukqu4e

Model quality assessment using distance constraints from alignments

Martin Paluszewski, Kevin Karplus
2009 Proteins: Structure, Function, and Bioinformatics  
A good MQA is crucial when one has to choose the best model among several different models-for example, in a metaserver for protein structure prediction.  ...  Metaservers use structure models generated by other methods and either choose one of the models using an MQA or construct a consensus model to make a predicted structure.  ...  The contact number predictions are done using the same neural network program (predict-2nd) that we use for all our local structure prediction [11] .  ... 
doi:10.1002/prot.22262 pmid:19003987 pmcid:PMC2670941 fatcat:lxymjn5snre7zgxog3c7x2yx3e

The ecology of tool-use in the woodpecker finch (Cactospiza pallida)

Sabine Tebbich, Michael Taborsky, Birgit Fessl, Michael Dvorak
2002 Ecology Letters  
Here, we present the first ecological study of tool-use by a bird species. Woodpecker finches use twigs or cactus spines to pry arthropods out of tree-holes.  ...  Insects, mammals and birds are known to use tools, but empirical evidence of the ecological importance of tool-use is scarce.  ...  A C K N O W L E D G E M E N T S We thank the Galápagos National Park Service, the Charles Darwin Research Station, TAME and especially W. Wickler for enabling this study; L.  ... 
doi:10.1046/j.1461-0248.2002.00370.x fatcat:n6wvwvid4rgwbftzz4ksibkqzi

Epigenome-wide association study of leukocyte telomere length

Yunsung Lee, Dianjianyi Sun, Anil P.S. Ori, Ake T. Lu, Anne Seeboth, Sarah E. Harris, Ian J. Deary, Riccardo E. Marioni, Mette Soerensen, Jonas Mengel-From, Jacob Hjelmborg, Kaare Christensen (+10 others)
2019 Aging  
Using a meta-analysis framework, we identified DNA methylation (DNAm) levels at 823 CpG sites to be significantly associated (P<1E-7) with LTL after adjusting for age, sex, ethnicity, and imputed white  ...  Functional enrichment analyses revealed that these CpG sites are near genes that play a role in circadian rhythm, blood coagulation, and wound healing.  ...  We also appreciate all the GEO submitters for making their DNAm data publically available.  ... 
doi:10.18632/aging.102230 pmid:31461406 pmcid:PMC6738430 fatcat:44jelcshbzgrhmlit2sfzfeppy

Persistence-Based Clustering in Riemannian Manifolds

Frédéric Chazal, Leonidas J. Guibas, Steve Y. Oudot, Primoz Skraba
2013 Journal of the ACM  
Thus, vp is a local maximum in Rδ (P).  ...  The Elements of Statistical Learning: Data Mining, nference, and Prediction 2nd Ed. Springer. atcher. 2001. Algebraic Topology. Cambridge University Press. http://www.math.cornell.edu/∼hatcher/.  ... 
doi:10.1145/2535927 fatcat:petxqjlqkrg3hio4xvueniupgy

Persistence-based clustering in riemannian manifolds

Frédéric Chazal, Leonidas J. Guibas, Steve Y. Oudot, Primoz Skraba
2011 Proceedings of the 27th annual ACM symposium on Computational geometry - SoCG '11  
Thus, vp is a local maximum in Rδ (P).  ...  The Elements of Statistical Learning: Data Mining, nference, and Prediction 2nd Ed. Springer. atcher. 2001. Algebraic Topology. Cambridge University Press. http://www.math.cornell.edu/∼hatcher/.  ... 
doi:10.1145/1998196.1998212 dblp:conf/compgeom/ChazalGOS11 fatcat:z3drfytzwrappaxcw5nyftxqdu

Tailored Analysis in Studying Transcriptome Landscape [article]

Xintian Arthur You, Universitätsbibliothek Der FU Berlin, Universitätsbibliothek Der FU Berlin
2015
Third, a de novo microRNA prediction tools is presented.  ...  By tailoring tools for long read-length sequencing technology, transcriptome landscape could be examined with greater detail.  ...  Predict 2nd structure We predicted the secondary structures of the selected long reads using RNAfold (parameters: -p -d 2 -noLP) [87] and randfold (parameter: -d 199) [88] , respectively.  ... 
doi:10.17169/refubium-14816 fatcat:jxj6jpv7a5btfgbs5pxdvv6mjy

In-silico models for the characterization of compounds interfering with clinical relevant ABC-multidrug-transporters

Michael Alexander Demel
2013 unpublished
Human ABC-transporters, which act as drug carriers, are notorious for their pivotal role in influencing the pharmacokinetic fate of a plethora of marketed drugs and also for their contribution to MDR,  ...  From a pharmacological viewpoint the thesis will concentrate on ABCB1.  ...  Especially the structure of Sav1866, which exhibits a higher resolution (3.0 Å) than the new MsbA structure (5.5 Å), has been immediately used as a template structure for the generation of protein homology  ... 
doi:10.25365/thesis.30426 fatcat:pkwghfepojf75ag3qerzsd3emm

The sensitivity of the cochlear amplifier to changes in operating conditions

Yi Wang
2019
Using a Boltzmann model and [...]  ...  Cochlear amplification was monitored by measuring the local cochlear microphonic (LCM) and distortion product emission (DPOAE).  ...  This is termed the local cochlear microphonic (LCM). The LCM is generated by local OHC responses, thus is a useful tool to detect cochlear amplification.  ... 
doi:10.7916/d8-r87p-0210 fatcat:7guk47o4vngung2dn7vaw3frdm