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Structural Requirements forin VivoMyosin I Function inAspergillus nidulans

Nir Osherov, Roxanne A. Yamashita, Yun-Shin Chung, Gregory S. May
1998 Journal of Biological Chemistry  
A., Gruver, C., and May, G. S. (1995) J.  ...  The resulting strains contained wild type myoA driven by the alcA promoter and a mutant myoA driven by its endogenous promoter.  ...  to form a colony (Fig. 5 ).  ... 
doi:10.1074/jbc.273.41.27017 pmid:9756952 fatcat:7bstqqxfbbfklh3umz3262lyji

NCBI's Conserved Domain Database and Tools for Protein Domain Analysis

Mingzhang Yang, Myra K. Derbyshire, Roxanne A. Yamashita, Aron Marchler‐Bauer
2019 Current Protocols in Bioinformatics  
The three protocols listed here describe how to perform a CD-Search (Basic Protocol 1), a Batch CD-Search (Basic Protocol 2), and a Standalone RPS-BLAST and rpsbproc (Basic Protocol 3). © 2019 The Authors  ...  It includes protein domain and protein family models curated in house by CDD staff, as well as imported from a variety of other sources.  ...  a domain hit.  ... 
doi:10.1002/cpbi.90 pmid:31851420 pmcid:PMC7378889 fatcat:lr3pkrp5qjfu5f76wiqs5tof5e

Constitutive Activation of Endocytosis by Mutation ofmyoA, the Myosin I Gene ofAspergillus nidulans

Roxanne A. Yamashita, Gregory S. May
1998 Journal of Biological Chemistry  
These studies are the first to demonstrate the in vivo significance of a regulatory phosphorylation on a class I myosin.  ...  A strain that has a temper-ature-sensitive myo5 mutation is defective for endocytosis but not for protein secretion (3) .  ...  A portion of the purified PCR product was used to prime a second reaction with the primers myoA24 and myoA7 to produce a product of 190 bp.  ... 
doi:10.1074/jbc.273.23.14644 pmid:9603982 fatcat:cmd7pnzntvdededuer3lzfjd2u

cddApp: a Cytoscape app for accessing the NCBI conserved domain database

John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin
2014 Computer applications in the biosciences : CABIOS  
Motivation: cddApp is a Cytoscape extension that supports the annotation of protein networks with information about domains and specific functional sites from the National Center for Biotechnology Information's  ...  If a PDB column was selected as part of the load and a PDB structure was annotated for a node, the Results Panel will also contain a checkbox to open that structure in UCSF Chimera (Pettersen et al.,  ...  of proteins in a network context.  ... 
doi:10.1093/bioinformatics/btu605 pmid:25212755 pmcid:PMC4271147 fatcat:2wwumnmptjeqxp4brys6mb2kxi

Identification of several novel Neurospora genes in the lambda-ZAP I and lambda-ZAP II libraries

Roxanne A. Yamashita, W. Dorsey Stuart
1996 Fungal Genetics Reports  
Primary sequencing of the identified phagemids revealed homologies to a number of known genes. These genes are listed and the cDNA clones are available from our laboratory to interested parties.  ...  Identification of several novel Neurospora crassa genes in the lambda-ZAP I and lambda-ZAP II libraries Roxanne A. Yamashita and W.  ...  A degenerate DNA probe was made to one band from a sucrose grown culture corresponding to a protein of approximately 14.4 kd.  ... 
doi:10.4148/1941-4765.1322 fatcat:ols5xjjvr5ecxp3mbgkuitfu7i

CDD: conserved domains and protein three-dimensional structure

Aron Marchler-Bauer, Chanjuan Zheng, Farideh Chitsaz, Myra K. Derbyshire, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu, Shennan Lu (+6 others)
2012 Nucleic Acids Research  
Figure 2 gives an example of a CD-Search graphical results summary obtained for a nucleotide query representing a complete viral genome.  ...  CD-Search results for a nucleotide query sequence, the complete genome sequence of a Hepatitis B virus.  ... 
doi:10.1093/nar/gks1243 pmid:23197659 pmcid:PMC3531192 fatcat:kyfhbmseffcrjpuj7ie33t7trq

CDD: NCBI's conserved domain database

Aron Marchler-Bauer, Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Farideh Chitsaz, Lewis Y. Geer, Renata C. Geer, Jane He, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu (+8 others)
2014 Nucleic Acids Research  
NCBI's CDD, the Conserved Domain Database, enters its 15 th year as a public resource for the annotation of proteins with the location of conserved domain footprints.  ...  The curation effort aims at increasing coverage and providing finergrained classifications of common protein domains, for which a wealth of functional and structural data has become available.  ...  Upcoming versions of CDD will contain a novel type of model, called a 'structural domain', with the accession prefix 'sd'.  ... 
doi:10.1093/nar/gku1221 pmid:25414356 pmcid:PMC4383992 fatcat:fmwggydorjhetcwv6griivaci4

RefSeq: an update on prokaryotic genome annotation and curation

Daniel H Haft, Michael DiCuccio, Azat Badretdin, Vyacheslav Brover, Vyacheslav Chetvernin, Kathleen O'Neill, Wenjun Li, Farideh Chitsaz, Myra K Derbyshire, Noreen R Gonzales, Marc Gwadz, Fu Lu (+9 others)
2017 Nucleic Acids Research  
Genomes are annotated by a single Prokaryotic Genome Annotation Pipeline (PGAP) to provide users with a resource that is as consistent and accurate as possible.  ...  Notable recent changes include the development of a hierarchical evidence scheme, a new focus on curating annotation evidence sources, the addition and curation of protein profile hidden Markov models  ...  A BlastRule requires only (i) a name to apply during annotation, (ii) one or more reference proteins to use in BLAST searches and (iii) parameters to determine if a BLAST match to a reference protein is  ... 
doi:10.1093/nar/gkx1068 pmid:29112715 pmcid:PMC5753331 fatcat:hgvzb5wly5flvfsj7wlev6myby

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

Aron Marchler-Bauer, Yu Bo, Lianyi Han, Jane He, Christopher J. Lanczycki, Shennan Lu, Farideh Chitsaz, Myra K. Derbyshire, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz (+10 others)
2016 Nucleic Acids Research  
CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from external providers, with representations of selected domain families  ...  CDD also supports comparative analyses of protein families via conserved domain architectures, and a recent curation effort focuses on providing functional characterizations of distinct subfamily architectures  ...  Here we present a first and simple implementation of that idea, which defines a Subfamily Domain Architecture as the string of the domain model accessions that provide the most concise annotation on a  ... 
doi:10.1093/nar/gkw1129 pmid:27899674 pmcid:PMC5210587 fatcat:uwnork4w2bfhrovmauui7o5ejm

Response to NIH Request for Information: Institutional Accountability to Promote Inclusive Excellence [article]

Diversity and Inclusion Committee Equality
2019 Zenodo  
Yamashita, NIH/NCBI, Bethesda, MD  ...  A response to the NIH Request for Information on Institutional Accountability to Promote Inclusive Excellence.  ...  A Code of Conduct is intended to establish a set of rules of expected behavior amongst members of a community.  ... 
doi:10.5281/zenodo.2875899 fatcat:e3ujxwu5hndlfnqz2aqsy2muya

Tubulin family: Kinship of key proteins across phylogenetic domains

Edward H Egelman
1998 Current Biology  
to form a helical polymer.  ...  lineage, a more complex, heterodimeric protein evolved from a single ancestral FtsZ-like precursor.  ...  A Yamashita and Gregory S May Myosins: matching functions with motors Jeffrey P Baker and Margaret A Titus The slow axonal transport of cytoskeletal proteins Ralph A Nixon Intermediate filaments and  ... 
doi:10.1016/s0960-9822(98)70175-7 pmid:9550697 fatcat:ucrrj6ws45es5hq2zeqenyqyum

Annotation of functional sites with the Conserved Domain Database

M. K. Derbyshire, C. J. Lanczycki, S. H. Bryant, A. Marchler-Bauer
2012 Database: The Journal of Biological Databases and Curation  
Yamashita, Chanjuan Zheng, as well as the CDD alumni Anastasia Conflict of interest.  ...  Acknowledgements We thank the Conserved Domain Curators for compiling the site annotations analyzed in this work, Farideh Chitsaz, Noreen Gonzales, Marc Gwadz, Fu Lu, Gabriele Marchler, James Song, Narmada Thanki, Roxanne  ...  particular region on a protein.  ... 
doi:10.1093/database/bar058 pmid:22434827 pmcid:PMC3308149 fatcat:xwt5xq6kwrgedmsbf7ujgsp32e

Antagonist-induced conformational changes in dopamine transporter extracellular loop two involve residues in a potential salt bridge

Jon D. Gaffaney, Madhur Shetty, Bruce Felts, Akula-Bala Pramod, James D. Foster, L. Keith Henry, Roxanne A. Vaughan
2014 Neurochemistry International  
structural basis for their similar conformational sensitivities and indicating their potential to form a salt bridge.  ...  In a previous study we demonstrated that ligand-induced protease resistance also occurred at R218 on the C-terminal side of rDAT EL2.  ...  Substrate and antagonist binding sites on DAT Substrate binding in LeuT Aa occurs in a pocket referred to as S1 that is formed between the extracellular and intracellular gates (Yamashita et al., 2005  ... 
doi:10.1016/j.neuint.2013.11.003 pmid:24269640 pmcid:PMC4394652 fatcat:lybazrvsxvdprhkajkhpihkj5q

Palmitoylation mechanisms in dopamine transporter regulation

Danielle E. Rastedt, Roxanne A. Vaughan, James D. Foster
2017 Journal of Chemical Neuroanatomy  
We have recently demonstrated the acute and chronic modulation of DA reuptake activity and DAT stability through S-palmitoylation, the linkage of a 16-carbon palmitate group to cysteine via a thioester  ...  The neurotransmitter dopamine (DA) plays a key role in several biological processes including reward, mood, motor activity and attention.  ...  It is also possible that palmitoylation of DAT at Cys580 may affect its ability to form a dimer, as the LeuT crystal structure showed a dimer interface at TMD12 (Yamashita et al., 2005) .  ... 
doi:10.1016/j.jchemneu.2017.01.002 pmid:28115272 pmcid:PMC6077000 fatcat:36bp6tga6ngp5k6nho5c2kqrgq

Acknowledgment to Reviewers of Pharmaceuticals in 2020

Pharmaceuticals Editorial Office Pharmaceuticals Editorial Office
2021 Pharmaceuticals  
Amorós, Asunción López, Óscar Anas, Andrea Roxanne J.  ...  A.  ... 
doi:10.3390/ph14020082 pmid:33499339 fatcat:ui3xa46jjfce7ee6vpx2r6nc2m
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