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Evolution of a computer program for classifying protein segments as transmembrane domains using genetic programming

J R Koza
1994 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
The recently-developed genetic programming paradigm is used to evolve a computer program to classify a given protein segment as being a transmembrane domain or non-transmembrane area of the protein.  ...  Genetic programming is given a training set of differently-sized protein segments and their correct classification (but no biochemical knowledge, such as hydrophobicity values).  ...  Rice of the Knowledge Systems Laboratory at Stanford University did the computer programming of the above on a Texas Instruments Explorer II + computer.  ... 
pmid:7584397 fatcat:alkidm6xdvfrhn2m3zhmffdilm

A case study where biology inspired a solution to a computer science problem

J R Koza, D Andre
1996 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
Genetic programming with the new architecture-altering operations was then applied to the transmembrane protein segment identification problem.  ...  The out-of-sample error rate for the best genetically-evolved program achieved was slightly better than that of previously-reported human-written algorithms for this problem.  ...  segment as a transmembrane domain; otherwise, classify it as a non-transmembrane area of the protein.  ... 
pmid:9390254 fatcat:2p453gcebjgubkocqmhqobq5m4

Membrane Porters of ATP-Binding Cassette Transport Systems Are Polyphyletic

Bin Wang, Maxim Dukarevich, Eric I. Sun, Ming Ren Yen, Milton H. Saier
2009 Journal of Membrane Biology  
Using five distinct computer programs, we here provide convincing statistical data suggesting that the transmembrane domains of ABC exporters are polyphyletic, having arisen at least three times independently  ...  ABC1 porters arose by intragenic triplication of a primordial two-transmembrane segment (TMS)-encoding genetic element, yielding six TMS proteins.  ...  Geoff Chang for valuable discussions; and the National Institutes of Health (GM077402) for financial support.  ... 
doi:10.1007/s00232-009-9200-6 pmid:19806386 fatcat:am5qjgyjfvetfiamtgihpqa2ku

Proteomics Computational Analyses Suggest That the Envelope Glycoproteins of Segmented Jingmen Flavi-Like Viruses are Class II Viral Fusion Proteins (b-Penetrenes) with Mucin-Like Domains

Courtney E. Garry, Robert F. Garry
2020 Viruses  
Computational analyses were used to predict that Jingmen flavi-like virus glycoproteins have structural features of class II viral fusion proteins, including an ectodomain consisting of beta-sheets and  ...  Some of the glycoproteins are predicted to have an additional mucin-like domain located prior to the transmembrane anchor, whereas others are predicted to have a stem consisting of two alpha-helices.  ...  Tulane University and its various academic and industry partners have filed US and foreign patent applications on behalf of the consortium for several of these technologies.  ... 
doi:10.3390/v12030260 pmid:32120884 pmcid:PMC7150890 fatcat:o3j6mzd54rbprhfe6sygyvboni

Computational Tools For Protein Modeling

Dong Xu, Ying Xu, Edward Uberbacher
2000 Current protein and peptide science  
This review attempts to provide a comprehensive introduction to major computer programs, especially on-line servers, for protein modeling.  ...  Protein modeling is playing a more and more important role in protein and peptide sciences due to improvements in modeling methods, advances in computer technology, and the huge amount of biological data  ...  Michael A. Unseren for a critical reading of this manuscript. We also thank Drs. Oakley H. Crawford  ... 
doi:10.2174/1389203003381469 pmid:12369918 fatcat:el6l7svg6jej3izdsuodtxocz4

Computational characterization of providence virus non-structural proteins: Evolutionary and functional implications
English

Ritah Nakayinga
2019 Journal of Bioinformatics and Sequence Analysis  
The purpose of this study is to identify sequences within these non-structural proteins with potential roles in replication and evolution using computational tools.  ...  Analysis of the p40 revealed a sequence with a coiled-coil conformation and surface-exposed characteristics comparable to the interaction domain of Tombusvirus, Tomato bushy stunt virus p33 accessory protein  ...  analyzed for its surface-exposed and hydrophilic properties using the Protscale program (http://web.expasy.org/protscale) using a window size of 5.  ... 
doi:10.5897/jbsa2019.0111 fatcat:ux3bb3mgmvb7bg4yi6rhm7slha

Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation

Fei Qi, Magdalena Motz, Kirsten Jung, Jürgen Lassak, Dmitrij Frishman, Charlotte M. Deane
2018 PLoS Computational Biology  
Against the overall trend of polyproline motif loss in evolution, we observed their enrichment in the vicinity of translational start sites, in the inter-domain regions of multi-domain proteins, and downstream  ...  Enrichment of polyproline motifs in the protein regions bracketing structural domains and transmembrane helices indicates their regulatory role in co-translational protein folding and transmembrane helix  ...  Acknowledgments We thank Peter Hönigschmid and Jianfeng Sun for constructive discussions. Author Contributions  ... 
doi:10.1371/journal.pcbi.1005987 pmid:29389943 pmcid:PMC5811046 fatcat:jnhyb47tfvcsdg2mzkdho4k2au

Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

M. R. Aniba, O. Poch, J. D. Thompson
2010 Nucleic Acids Research  
To illustrate these principles, we present a more detailed discussion of benchmarks for multiple alignments of protein sequences.  ...  As in many other domains, significant progress has been achieved in the multiple alignment field and the datasets have become progressively more challenging as the existing algorithms have evolved.  ...  ACKNOWLEDGEMENTS The authors would like to thank the members of the Laboratory of Integrative Bioinformatics and Genomics (LBGI) for many fruitful discussions and the Strasbourg Bioinformatics Platform  ... 
doi:10.1093/nar/gkq625 pmid:20639539 pmcid:PMC2995051 fatcat:nfxihponuzedjosm6cwgcccjee

Genome Organization of the SARS-CoV

Jing Xu, Jianfei Hu, Jing Wang, Yujun Han, Yongwu Hu, Jie Wen, Yan Li, Jia Ji, Jia Ye, Zizhang Zhang, Wei Wei, Songgang Li (+4 others)
2003 Genomics, Proteomics & Bioinformatics  
We have performed a full annotation of the SARS-CoV genome sequences by using annotation programs publicly available or developed by ourselves.  ...  Totally, 21 open reading frames (ORFs) of genes or putative uncharacterized proteins (PUPs) were predicted.  ...  We are grateful to Jinsong Liu for providing the BGFV program and mathematical calculations.  ... 
doi:10.1016/s1672-0229(03)01028-3 fatcat:oqa5h7tr7zcvvmu4bje3zm6zku

Introduction to genetic programming

John R. Koza
2008 Proceedings of the 2008 GECCO conference companion on Genetic and evolutionary computation - GECCO '08  
array of pixels GECCO 2007 Tutorial / Introduction to Genetic Programming 44 REUSE-TRANSMEMBRANE SEGMENT IDENTIFICATION PROBLEM • Goal is to classify a given protein segment as being a transmembrane domain  ...  Using genetic programming (GP), we can solve the general, by searching the space of computer programs for a program that takes a, b, and c as inputs The result is a solution to ALL INSTANCES of the quadratic  ...  learning, adaptive systems, and automated learning can be recast as a search for a computer program. • Genetic programming provides a way to successfully conduct the search for a computer program in the  ... 
doi:10.1145/1388969.1389057 dblp:conf/gecco/Koza08 fatcat:zguwd4zecre7rfldh7zywhaluy

Topology of yeast Ndc1p: Predictions for the human NDC1/NET3 homologue

Corine K. Lau, Valerie A. Delmar, Douglass J. Forbes
2006 Anatomical Record Part A-discoveries in Molecular Cellular and Evolutionary Biology  
We show that the overall topology of these homologues is conserved. Each contains six transmembrane segments in its N-terminal half and has a large soluble C-terminal half of ϳ 300 amino acids.  ...  Moreover, a small region containing mutations that affect assembly of the nuclear pore in yeast is highly conserved throughout evolution.  ...  ACKNOWLEDGMENTS The authors thank Alexander Shearer and Randy Hampton for technical help and the Hmg2p constructs, Laura Kwinn and Victor Nizet for the use of the AlignX software, and Mark Winey for the  ... 
doi:10.1002/ar.a.20335 pmid:16779818 pmcid:PMC3049984 fatcat:3viw4x5y6nbwnpo6wsz72zguv4

Evolutionary relationships of the Tas2r receptor gene families in mouse and human

Caroline Conte, Martin Ebeling, Anne Marcuz, Patrick Nef, Pedro J. Andres-Barquin
2003 Physiological Genomics  
Slack, Ping Zhong, and Gonzalo Acuñ a for helpful discussions.  ...  The resulting alignment was graphically displayed using the PrettyBox program from the Wisconsin Package Version 10.2, Genetics Computer Group (GCG), Madison, WI.  ...  Sequence analysis of the new proteins also indicated the presence of seven transmembrane domains and large sequence conservation in the transmembrane domains and in the intracellular domains.  ... 
doi:10.1152/physiolgenomics.00060.2003 pmid:12734386 fatcat:uu4yti3vqfh7vogl5n454kypwm

Prediction of G Protein Coupled Receptors from Plant Genomes

Deisy Xavier Amora, Emmanuel Bresso, Roberto Coiti Togawa, Priscila Grynberg, Bernard Maigret, tália Florêncio Martins
2016 International Journal of Current Research in Biosciences and Plant Biology  
G-protein coupled receptors (GPCRs) are the largest family of membrane proteins, as key components of signal transduction pathways.  ...  The availability of plant genomes allows the prediction and characterization of diverse GPCRs, as for several species the repertoire of GPCRs remains unclear.  ...  Acknowledgement Work in Bioinformatics Lab at Embrapa Genetic Resources and Biotechnology is supported by Grants numbers: CNPq Grant # 454064/2014-4, CAPES Grant # 51/2013.  ... 
doi:10.20546/ijcrbp.2016.311.014 fatcat:ru7w24wvizg2jllciheuomfseq

Modular arrangement of proteins as inferred from analysis of homology

Erik L.L. Sonnhammer, Daniel Kahn
2008 Protein Science  
These nonredundant domain consensuses are useful for fast homology searches.  ...  The structure of many proteins consists of a combination of discrete modules that have been shuffled during evolution. Such modules can frequently be recognized from the analysis of homology.  ...  the art of programming in C.  ... 
doi:10.1002/pro.5560030314 pmid:8019419 pmcid:PMC2142695 fatcat:pvhytyupb5hlrjmbflhuqgbspe

MACSIMS: multiple alignment of complete sequences information management system

Julie D Thompson, Arnaud Muller, Andrew Waterhouse, Jim Procter, Geoffrey J Barton, Frédéric Plewniak, Olivier Poch
2006 BMC Bioinformatics  
MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases.  ...  An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis.  ...  We are grateful to Anne Friedrich and Luc Moulinier for their help with the MS2PH test set.  ... 
doi:10.1186/1471-2105-7-318 pmid:16792820 pmcid:PMC1539025 fatcat:ceiagxqwrbgajohiyh5szo5zgq
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