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List of works by Thomas E Ferrin

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

scientific article

An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences

scientific article published on 5 January 2017

Annotating PDB files with scene information

scientific article published in June 1995

Automated site-directed drug design using molecular lattices ⬇️

scientific article published on June 1, 1992

BayGenomics: a resource of insertional mutations in mouse embryonic stem cells

scientific article published on January 2003

Biocuration in the structure-function linkage database: the anatomy of a superfamily

scientific article

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

scientific article

Clinical Persistence of Chlamydia trachomatis Sexually Transmitted Strains Involves Novel Mutations in the Functional αββα Tetramer of the Tryptophan Synthase Operon

scientific article published on 16 July 2019

Comparison of human solute carriers

scientific article

Comparison of methods for genomic localization of gene trap sequences

scientific article published on 18 September 2006

Computational tools for the interactive exploration of proteomic and structural data.

scientific article

Computer graphics in drug design: molecular modeling of thyroid hormone-prealbumin interactions

article

CyAnimator: Simple Animations of Cytoscape Networks

scientific article

DASP3: identification of protein sequences belonging to functionally relevant groups

scientific article

Designed divergent evolution of enzyme function

scientific article

Engineering cotton (+)-delta-cadinene synthase to an altered function: germacrene D-4-ol synthase

scientific article published in January 2006

Enhancing UCSF Chimera through web services

scientific article

Enhancing data sharing in collaborative research projects with DASH.

scientific article

Evolutionary conservation predicts function of variants of the human organic cation transporter, OCT1 ⬇️

scientific article published on April 28, 2003

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

scientific article published on 25 November 2019

Functional analysis of polymorphisms in the organic anion transporter, SLC22A6 (OAT1).

scientific article

Functional and genetic diversity in the concentrative nucleoside transporter, CNT1, in human populations

scientific article

Functional characterization and haplotype analysis of polymorphisms in the human equilibrative nucleoside transporter, ENT2

scientific article

Functional characterization in yeast of genetic variants in the human equilibrative nucleoside transporter, ENT1 ⬇️

scientific article published on May 1, 2003

Functional effects of protein sequence polymorphisms in the organic cation/ergothioneine transporter OCTN1 (SLC22A4).

scientific article

Functional genetic diversity in the high-affinity carnitine transporter OCTN2 (SLC22A5).

scientific article

Functional genetic variation in the basal promoter of the organic cation/carnitine transporters OCTN1 (SLC22A4) and OCTN2 (SLC22A5).

scientific article published on 13 January 2009

Genetic analysis and functional characterization of polymorphisms in the human concentrative nucleoside transporter, CNT2.

scientific article

Genetic variants in multidrug and toxic compound extrusion-1, hMATE1, alter transport function

scientific article

Genetic variants of human organic anion transporter 4 demonstrate altered transport of endogenous substrates ⬇️

scientific article published on July 28, 2010

Genetic variation in the proximal promoter of ABC and SLC superfamilies: liver and kidney specific expression and promoter activity predict variation ⬇️

scientific article

High-Performance Computing for Computational Biology

Identification and characterization of novel polymorphisms in the basal promoter of the human transporter, MATE1

scientific article

Identification and characterization of proximal promoter polymorphisms in the human concentrative nucleoside transporter 2 (SLC28A2).

scientific article published on 19 December 2008

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution

scientific article

Integrated tools for structural and sequence alignment and analysis

scientific article published on January 2000

Interaction of methotrexate with organic-anion transporting polypeptide 1A2 and its genetic variants

scientific article published on 15 May 2006

Interactive computer graphics with the UNIX time-sharing system

article

Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database

scientific article

MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance.

scientific article

MODBASE, a database of annotated comparative protein structure models, and associated resources.

scientific article

Macromolecular Assembly Structures by Comparative Modeling and Electron Microscopy ⬇️

scientific article published on January 1, 2012

ModBase, a database of annotated comparative protein structure models, and associated resources

scientific article

Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells

scientific article published on 18 July 2007

Molecular Visualization on the Holodeck

scientific article published on 28 June 2018

Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins

scientific article published on May 2015

Natural variation in human membrane transporter genes reveals evolutionary and functional constraints

scholarly article

Nucleic acid visualization with UCSF Chimera

scientific article

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

scientific article published on 18 June 2015

PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network

scientific article published in March 2006

PharmGKB submission update: V. PMT submissions of genetic variation in SLC22 family transporters

scientific article

PharmGKB submission update: VI. PMT submissions of genetic variations in neurotransmitter transporters (SLC6, SLC17, and SLC18) to the PharmGKB network

scientific article published in March 2006

PharmGKB update: I. Genetic variants of the organic cation transporter 2 (OCT2, SLC22A2).

scientific article

PharmGKB update: III. Genetic variants of SLC22A1, solute carrier family 22 (organic cation transporter), member 1.

scientific article published in June 2004

Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function

scientific article (publication date: July 2002)

RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps

scientific article published on 24 December 2014

Reply to Rockey et al., "Genomics and Chlamydial Persistence In Vivo"

scientific article published on 17 December 2019

Representing structure-function relationships in mechanistically diverse enzyme superfamilies.

scientific article published in January 2005

Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin

scientific article

SNP analysis and presentation in the Pharmacogenetics of Membrane Transporters Project.

scientific article

Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene

scientific article published on 01 August 2003

Software extensions to UCSF chimera for interactive visualization of large molecular assemblies

scientific article (publication date: March 2005)

The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse

scientific article

The Structure Superposition Database

scientific article published on January 2003

The Structure-Function Linkage Database

scientific article

The human multidrug resistance protein 4 (MRP4, ABCC4): functional analysis of a highly polymorphic gene

scientific article published on 25 March 2008

The human organic anion transporter 3 (OAT3; SLC22A8): genetic variation and functional genomics

scientific article

Tools for integrated sequence-structure analysis with UCSF Chimera

scientific article

UCSF Chimera, MODELLER, and IMP: an integrated modeling system

scientific article

UCSF Chimera--a visualization system for exploratory research and analysis

scientific article (publication date: October 2004)

UCSF ChimeraX: Meeting Modern Challenges in Visualization and Analysis.

scientific article published on 14 July 2017

UCSF ChimeraX: Structure Visualization for Researchers, Educators, and Developers

scientific article published on 03 September 2020

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

scientific article

Visualization software for molecular assemblies

scientific article

Workshop on molecular animation

scientific article

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

scientific article

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

scientific article

enhancedGraphics: a Cytoscape app for enhanced node graphics

scientific article published on July 2014

setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges.

scientific article published on July 2014

structureViz: linking Cytoscape and UCSF Chimera.

scientific article

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