Faculty

Institution

Unit

Venue

Thomas Ferrin

University of California, San Francisco

Affiliations

University of California San Francisco, Research

NoneThomas Ferrin is currently serving as a University Of California San Francisco, Research faculty at University of California, San Francisco.

Honors

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Experiences

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Education

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Thomas Ferrin

University of California, San Francisco

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molecular biology systems biology genetics bioinformatics protein science computational biology molecular informatics structural biology biomolecular engineering molecular modelling protein structure genomics structural molecular biology structural bioinformatics protein modeling molecular science protein bioinformatics molecular structure biomolecular structure pharmacological research molecular genetics scientific computing molecular graphics human polymorphisms human genetics genome biology medicinal research pharmacogenomics ucsf chimera knowledge discovery sequence analysis biological network visualization protein transport genetic variants machine learning research scientific visualization allelic variant sequence alignment computational biophysics information visualization peptides proteome research interactive visualization membrane transport biophysical modeling structure-function linkage database functional characterization pharmgkb submission update molecular modeling biological macromolecules protein structure prediction structure elucidation variant interpretation protein assembly biomolecular structure prediction medical genetics experimental pharmacology key site molecular design basal promoter cytoscape nodes relevant clustering pharmgkb network pmt submissions pharmgkb update visual data mining visual analytics biomolecular interactions reflective middleware display technology advanced display technology adaptive middleware visualization system structure visualization ucsf chimerax structure building

Notable Scholarly Works

Notable Federal Grants

Collaborators

IHMCIF: An Extension of the Pdbx/Mmcif Data Standard for Integrative Structure Determination Methods. Journal of Molecular Biology (2024)

Brinda VallatBenjamin M. WebbJohn D. WestbrookThomas D. GoddardChristian A. HankeAndrea GraziadeiEzra PeisachArthur ZalevskyJared SagendorfHongsuda TangmunarunkitSerban VoineaMonica SekharanJian YuAlexander A.M.J.J. BonvinFrank DiMaioGerhard HummerJens MeilerEmad TajkhorshidThomas E. FerrinCatherine L. LawsonAlexander LeitnerJuri RappsilberClaus A.M. SeidelCy M. JeffriesStephen K. BurleyJeffrey C. HochGenji KurisuKyle MorrisArdan PatwardhanSameer VelankarTorsten SchwedeJill TrewhellaCarl KesselmanHelen M. BermanAndrej Sali

protein sciencebiomolecular structurepdbx/mmcif data standardstructural biologyprotein modelingtask forcestructural bioinformaticsmolecular biologyprotein structuresystems biologystructural molecular biologybioinformaticsihmcif extension

Ucsf Chimerax: Tools for Structure Building and Analysis. Protein Science (2023)

Elaine C. MengThomas D. GoddardEric F. PettersenGreg S. CouchZach J. PearsonJohn H. MorrisThomas E. Ferrin

protein structure predictioncomputational biologyprotein sciencestructural biologyprotein modelingbioanalysisstructural bioinformaticsstructure elucidationprotein bioinformaticsprotein structuresystems biologystructure buildingbioinformatics

Ucsf Chimerax: Structure Visualization for Researchers, Educators, and Developers. Protein Science (2020)

Eric F. PettersenThomas D. GoddardConrad C. HuangElaine C. MengGregory S. CouchTristan I. CrollJohn H. MorrisThomas E. Ferrin

protein sciencecomputer sciencestructure visualizationvisualization

Clinical Persistence of Chlamydia Trachomatis Sexually Transmitted Strains Involves Novel Mutations in the Functional αββα Tetramer of the Tryptophan Synthase Operon. mBio (2019)

Naraporn SomboonnaNoa ZikloThomas E. FerrinJung Hyuk SuhDeborah Dean

chlamydia trachomatisinfectious diseasesfunctional abba tetramerpathogenic bacteriaclinical persistencepathogenesismicrobiologydiagnostic microbiologynovel mutationstryptophan synthase operonmicrobial pathogenesis

Federating Structural Models and Data: Outcomes From a Workshop on Archiving Integrative Structures. Structure (2019)

Helen M. BermanPaul D. AdamsAlexandre A. BonvinStephen K. BurleyBridget CarragherWah ChiuFrank DiMaioThomas E. FerrinMargaret J. GabanyiThomas D. GoddardPatrick R. GriffinJuergen HaasChristian A. HankeJeffrey C. HochGerhard HummerGenji KurisuCatherine L. LawsonAlexander LeitnerJohn L. MarkleyJens MeilerGaetano T. MontelioneGeorge N. PhillipsThomas PrisnerJuri RappsilberDavid C. SchriemerTorsten SchwedeClaus A.M. SeidelTimothy S. StrutzenbergDmitri I. SvergunEmad TajkhorshidJill TrewhellaBrinda VallatSameer VelankarGeerten W. VuisterBenjamin WebbJohn D. WestbrookKate L. WhiteAndrej Sali

administrative sciencesystematics (systems theory)structural modelsa workshopresearch data archivingsocial sciencesarchiving integrative structuresinformation sciencestructural probleminformation managementdigital scholarshipmanagementsocial systems

Reply to Rockey Et Al., “Genomics and Chlamydial Persistence in Vivo ”. mBio (2019)

Deborah DeanNoa ZikloNaraporn SomboonnaJung Hyuk SuhThomas Ferrin

molecular biologygenomics

Molecular Visualization on the Holodeck. Journal of Molecular Biology (2018)

Thomas D. GoddardAlan A. BrilliantThomas L. SkillmanSteven VergenzJames Tyrwhitt-DrakeElaine C. MengThomas E. Ferrin

single-molecule detectionbiological network visualizationstructural molecular biologymolecular researchmolecular graphicsmolecular sciencemolecular biophysicsmolecular biologybiomolecular structuremolecular imagingmolecular informaticsprotein structuresystems biologysingle molecule biophysicsstructural biologymolecular visualizationbiophysicsmolecular modellingmolecular structure

Actin-Based Protrusions of Migrating Neutrophils Are Intrinsically Lamellar and Facilitate Direction Changes. eLife (2017)

Lillian K Fritz-LaylinMegan Riel-MehanBi-Chang ChenSamuel J LordThomas D GoddardThomas E FerrinSusan M Nicholson-DykstraHenry HiggsGraham T JohnsonEric BetzigR Dyche Mullins

immunologymembrane biologyactin-based protrusionsevolutionary biologycell motilitycell migration

An Approach to Functionally Relevant Clustering of the Protein Universe: Active Site Profile-Based Clustering of Protein Structures and Sequences. Protein Science (2017)

Stacy T. KnutsonBrian M. WestwoodJanelle B. LeuthaeuserBrandon E. TurnerDon NguyendacGabrielle SheaKiran KumarJulia D. HaydenAngela F. HarperShoshana D. BrownJohn H. MorrisThomas E. FerrinPatricia C. BabbittJacquelyn S. Fetrow

protein bioinformaticsstructural molecular biologybioinformaticsclusteringrelevant clusteringmolecular biologyprotein structure predictioncomputational biologybiomolecular structureprotein modelingmolecular informaticsprotein structuresystems biologystructural biologyprotein sciencebiomolecular structure predictionstructural bioinformaticsprotein universemolecular structurebiomolecular engineering

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Computational Biology (2017)

Angela F. HarperJanelle B. LeuthaeuserPatricia C. BabbittJohn H. MorrisThomas E. FerrinLeslie B. PooleJacquelyn S. Fetrow

proteomicsscientific computingprotein bioinformaticsstructural molecular biologybioinformaticsrelevant clusteringmolecular biologycomputational biologyprotein modelingmolecular informaticspathway analysisprotein structuresystems biologyproteome researchprotein sciencemolecular modellinglarge-scale datasetsstructural bioinformaticsbiomolecular engineering

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Thomas Ferrin

University of California, San Francisco

Affiliations

University of California San Francisco, Research

NoneThomas Ferrin is currently serving as a University Of California San Francisco, Research faculty at University of California, San Francisco.

Honors

Create free account to unlock more features

Experiences

Create free account to unlock more features

Education

Create free account to unlock more features

Thomas Ferrin

University of California, San Francisco

You can click a keyword to filter the displayed items

Notable Scholarly Works

Notable Federal Grants

Collaborators

IHMCIF: An Extension of the Pdbx/Mmcif Data Standard for Integrative Structure Determination Methods. Journal of Molecular Biology (2024)

Ucsf Chimerax: Tools for Structure Building and Analysis. Protein Science (2023)

Elaine C. MengThomas D. GoddardEric F. PettersenGreg S. CouchZach J. PearsonJohn H. MorrisThomas E. Ferrin

Ucsf Chimerax: Structure Visualization for Researchers, Educators, and Developers. Protein Science (2020)

Eric F. PettersenThomas D. GoddardConrad C. HuangElaine C. MengGregory S. CouchTristan I. CrollJohn H. MorrisThomas E. Ferrin

protein sciencecomputer sciencestructure visualizationvisualization

Clinical Persistence of Chlamydia Trachomatis Sexually Transmitted Strains Involves Novel Mutations in the Functional αββα Tetramer of the Tryptophan Synthase Operon. mBio (2019)

Naraporn SomboonnaNoa ZikloThomas E. FerrinJung Hyuk SuhDeborah Dean

Federating Structural Models and Data: Outcomes From a Workshop on Archiving Integrative Structures. Structure (2019)

Reply to Rockey Et Al., “Genomics and Chlamydial Persistence in Vivo ”. mBio (2019)

Deborah DeanNoa ZikloNaraporn SomboonnaJung Hyuk SuhThomas Ferrin

molecular biologygenomics

Molecular Visualization on the Holodeck. Journal of Molecular Biology (2018)

Thomas D. GoddardAlan A. BrilliantThomas L. SkillmanSteven VergenzJames Tyrwhitt-DrakeElaine C. MengThomas E. Ferrin

Actin-Based Protrusions of Migrating Neutrophils Are Intrinsically Lamellar and Facilitate Direction Changes. eLife (2017)

Lillian K Fritz-LaylinMegan Riel-MehanBi-Chang ChenSamuel J LordThomas D GoddardThomas E FerrinSusan M Nicholson-DykstraHenry HiggsGraham T JohnsonEric BetzigR Dyche Mullins

immunologymembrane biologyactin-based protrusionsevolutionary biologycell motilitycell migration

An Approach to Functionally Relevant Clustering of the Protein Universe: Active Site Profile-Based Clustering of Protein Structures and Sequences. Protein Science (2017)

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Computational Biology (2017)

Angela F. HarperJanelle B. LeuthaeuserPatricia C. BabbittJohn H. MorrisThomas E. FerrinLeslie B. PooleJacquelyn S. Fetrow

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