0000000000455264

AUTHOR

Kiersten M. Ruff

showing 2 related works from this author

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins

2020

Abstract The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptor…

MESH: Databases ProteinMESH: Search EngineAcademicSubjects/SCI00010[SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry Molecular Biology/Structural Biology [q-bio.BM][SDV]Life Sciences [q-bio]media_common.quotation_subjectBiologycomputer.software_genreIntrinsically disordered proteins03 medical and health sciencesDatabases0302 clinical medicineInformation and Computing SciencesGeneticsFeature (machine learning)Database IssueHumansDatabases ProteinRepresentation (mathematics)Function (engineering)MESH: Tumor Suppressor Protein p53ComputingMilieux_MISCELLANEOUS030304 developmental biologymedia_commonGraphical user interfaceStructure (mathematical logic)MESH: Intrinsically Disordered Proteins0303 health sciencesMESH: HumansDatabase[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry Molecular Biology/Structural Biology [q-bio.BM]business.industryProteinBiological Sciences[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]MetadataSearch EngineIntrinsically Disordered ProteinsState (computer science)Generic health relevanceTumor Suppressor Protein p53businesscomputer030217 neurology & neurosurgeryEnvironmental SciencesDevelopmental Biology
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Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

2018

Editors at Science requested our input on the above discussion (comment by Best et al . and response by Riback et al .) because both sets of authors use our data from Fuertes et al . (2017) to support their arguments. The topic of discussion pertains to the discrepant inferences drawn from SAXS versus FRET measurements regarding the dimensions of intrinsically disordered proteins (IDPs) in aqueous solvents. Using SAXS measurements on labeled and unlabeled proteins, we ruled out the labels used for FRET measurements as the cause of discrepant inferences between the two methods. Instead, we propose that FRET and SAXS provide complementary readouts because of a decoupling of size and shape fl…

0301 basic medicinePhysicsMultidisciplinarySmall-angle X-ray scatteringScattering010402 general chemistryIntrinsically disordered proteins01 natural sciences0104 chemical sciences03 medical and health sciences030104 developmental biologyFörster resonance energy transferStatistical physicsDecoupling (electronics)Science
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