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1

UCSF Chimera—A visualization system for exploratory research and analysis

Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 323 KB

english, 2004

2

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

Holliday, Gemma L., Brown, Shoshana D., Akiva, Eyal, Mischel, David, Hicks, Michael A., Morris, John H., Huang, Conrad C., Meng, Elaine C., Pegg, Scott C.-H., Ferrin, Thomas E., Babbitt, Patricia C.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.30 MB

english, 2017

3

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

Holliday, Gemma L., Brown, Shoshana D., Akiva, Eyal, Mischel, David, Hicks, Michael A., Morris, John H., Huang, Conrad C., Meng, Elaine C., Pegg, Scott C.-H., Ferrin, Thomas E., Babbitt, Patricia C.

Journal:

Year:

2017

Language:

english

File:

PDF, 177 KB

english, 2017

4

The MIDAS display system

Thomas E. Ferrin, Conrad C. Huang, Laurie E. Jarvis, Robert Langridge

Journal:

Journal of Molecular Graphics

Year:

1988

Language:

english

File:

PDF, 1.31 MB

english, 1988

5

Visualizing density maps with UCSF Chimera

Thomas D. Goddard, Conrad C. Huang, Thomas E. Ferrin

Journal:

Journal of Structural Biology

Year:

2007

Language:

english

File:

PDF, 1.12 MB

english, 2007

6

A geometric approach to macromolecule-ligand interactions

Irwin D. Kuntz, Jeffrey M. Blaney, Stuart J. Oatley, Robert Langridge, Thomas E. Ferrin

Journal:

Journal of Molecular Biology

Year:

1982

Language:

english

File:

PDF, 17.82 MB

english, 1982

7

The MIDAS database system

Thomas E. Ferrin, Conrad C. Huang, Laurie E. Jarvis, Robert Langridge

Journal:

Journal of Molecular Graphics

Year:

1988

Language:

english

File:

PDF, 1.26 MB

english, 1988

8

A real-time malleable molecular surface

Teri E. Klein, Conrad C. Huang, Eric F. Pettersen, Gregory S. Couch, Thomas E. Ferrin, Robert Langridge

Journal:

Journal of Molecular Graphics

Year:

1990

Language:

english

File:

PDF, 939 KB

english, 1990

9

Conic: A fast renderer for spacefilling molecules with shadows

Conrad C. Huang, Eric F. Pettersen, Teri E. Klein, Thomas E. Ferrin, Robert Langridge

Journal:

Journal of Molecular Graphics

Year:

1991

Language:

english

File:

PDF, 855 KB

english, 1991

10

Molecular image representations and their uses

Thomas Ferrin, Robert Langridge

Journal:

Journal of Molecular Graphics

Year:

1992

Language:

english

File:

PDF, 143 KB

english, 1992

11

Automated site-directed drug design using molecular lattices

Richard A. Lewis, Diana C. Roe, Conrad Huang, Thomas E. Ferrin, Robert Langridge, Irwin D. Kuntz

Journal:

Journal of Molecular Graphics

Year:

1992

Language:

english

File:

PDF, 1.58 MB

english, 1992

12

Annotating PDB files with scene information

Gregory S. Couch, Eric F. Pettersen, Conrad C. Huang, Thomas E. Ferrin

Journal:

Journal of Molecular Graphics

Year:

1995

Language:

english

File:

PDF, 631 KB

english, 1995

13

Engineering Cotton (+)-δ-Cadinene Synthase to an Altered Function: Germacrene D-4-ol Synthase

Yasuo Yoshikuni, Vincent J.J. Martin, Thomas E. Ferrin, Jay D. Keasling

Journal:

Chemistry & Biology

Year:

2006

Language:

english

File:

PDF, 328 KB

english, 2006

14

clusterMaker:a multi-algorithm clustering plugin for Cytoscape

John H Morris, Leonard Apeltsin, Aaron M Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D Bader, Thomas E Ferrin

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 5.02 MB

english, 2011

15

Comparison of human solute carriers

Avner Schlessinger, Pär Matsson, James E. Shima, Ursula Pieper, Sook Wah Yee, Libusha Kelly, Leonard Apeltsin, Robert M. Stroud, Thomas E. Ferrin, Kathleen M. Giacomini, Andrej Sali

Journal:

Protein Science

Year:

2010

Language:

english

File:

PDF, 1.79 MB

english, 2010

16

Designed divergent evolution of enzyme function

Yoshikuni, Yasuo, Ferrin, Thomas E., Keasling, Jay D.

Journal:

Year:

2006

Language:

english

File:

PDF, 548 KB

english, 2006

17

Evaluation of Bioequivalence of Highly Variable Drugs Using Clinical Trial Simulations. II: Comparison of Single and Multiple-Dose Trials Using AUC and Cmax

Ahmed A. El-Tahtawy, Thomas N. Tozer, Ferrin Harrison, Larry Lesko, Roger Williams

Journal:

Pharmaceutical Research

Year:

1998

File:

PDF, 727 KB

1998

18

Visualization software for molecular assemblies

Thomas D Goddard, Thomas E Ferrin

Journal:

Current Opinion in Structural Biology

Year:

2007

Language:

english

File:

PDF, 4.18 MB

english, 2007

19

Software Extensions to UCSF Chimera for Interactive Visualization of Large Molecular Assemblies

Thomas D. Goddard, Conrad C. Huang, Thomas E. Ferrin

Journal:

Year:

2005

Language:

english

File:

PDF, 718 KB

english, 2005

20

Workshop on Molecular Animation

Sarina Bromberg, Wah Chiu, Thomas E. Ferrin

Journal:

Year:

2010

Language:

english

File:

PDF, 116 KB

english, 2010

21

Tools for integrated sequence-structure analysis with UCSF Chimera

Elaine C Meng, Eric F Pettersen, Gregory S Couch, Conrad C Huang, Thomas E Ferrin

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 671 KB

english, 2006

22

Comparison of methods for genomic localization of gene trap sequences

Courtney A Harper, Conrad C Huang, Doug Stryke, Michiko Kawamoto, Thomas E Ferrin, Patricia C Babbitt

Journal:

Year:

2006

Language:

english

File:

PDF, 1.21 MB

english, 2006

23

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

Zheng Yang, Keren Lasker, Dina Schneidman-Duhovny, Ben Webb, Conrad C. Huang, Eric F. Pettersen, Thomas D. Goddard, Elaine C. Meng, Andrej Sali, Thomas E. Ferrin

Journal:

Journal of Structural Biology

Year:

2012

Language:

english

File:

PDF, 2.50 MB

english, 2012

24

Interactive computer graphics with the UNIX time-sharing system

Ferrin, Thomas E., Langridge, Robert

Journal:

ACM SIGGRAPH Computer Graphics

Year:

1980

Language:

english

File:

PDF, 886 KB

english, 1980

25

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

Blaney, Jeffrey M., Jorgensen, Eugene C., Connolly, Michael L., Ferrin, Thomas E., Langridge, Robert, Oatley, Stuart J., Burridge, Jane M., Blake, Colin C. F.

Journal:

Journal of Medicinal Chemistry

Year:

1982

Language:

english

File:

PDF, 3.27 MB

english, 1982

26

Leveraging Enzyme Structure−Function Relationships for Functional Inference and Experimental Design: The Structure−Function Linkage Database †

Pegg, Scott C.-H., Brown, Shoshana D., Ojha, Sunil, Seffernick, Jennifer, Meng, Elaine C., Morris, John H., Chang, Patricia J., Huang, Conrad C., Ferrin, Thomas E., Babbitt, Patricia C.

Journal:

Year:

2006

Language:

english

File:

PDF, 285 KB

english, 2006

27

Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins

Hertig, Samuel, Goddard, Thomas D., Johnson, Graham T., Ferrin, Thomas E.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 1.16 MB

english, 2015

28

SPIE Proceedings [SPIE Medical Imaging '91, San Jose, CA - San Jose, CA (Sunday 24 February 1991)] Large Screen Projection, Avionic, and Helmet-Mounted Displays - Survey of helmet tracking technologies

Ferrin, Frank J., Assenheim, Harry M., Flasck, Richard A., Lippert, Thomas M., Bentz, Jerry

Year:

1991

Language:

english

File:

PDF, 265 KB

english, 1991

29

[ACM Press the SIGCHI conference - Monterey, California, United States (1992.05.03-1992.05.07)] Proceedings of the SIGCHI conference on Human factors in computing systems - CHI '92 - The MidasPlus molecular modeling system

Ferrin, Thomas, Huang, Conrad, Couch, Gregory, Pettersen, Eric, Langridge, Robert

Year:

1992

Language:

english

File:

PDF, 134 KB

english, 1992

30

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

Chen, Ying, Teranishi, Kristen, Li, Shuanglian, Yee, Sook Wah, Hesselson, Stephanie, Stryke, Doug, Johns, Susan J, Ferrin, Thomas E, Kwok, Pui, Giacomini, Kathleen M

Journal:

The Pharmacogenomics Journal

Year:

2009

Language:

english

File:

PDF, 540 KB

english, 2009

31

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

Osato, Douglas H, Huang, Conrad C, Kawamoto, Michiko, Johns, Susan J, Stryke, Doug, Wang, Joanne, Ferrin, Thomas E, Herskowitz, Ira, Giacomini, Kathleen M

Journal:

Pharmacogenetics

Year:

2003

Language:

english

File:

PDF, 170 KB

english, 2003

32

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

Leabman, Maya K., Huang, Conrad C., Kawamoto, Michiko, Johns, Susan J., Stryke, Douglas, Ferrin, Thomas E., DeYoung, Joseph, Taylor, Travis, Clark, Andrew G., Herskowitz, Ira, Giacomini, Kathleen M.

Journal:

Pharmacogenetics

Year:

2002

Language:

english

File:

PDF, 350 KB

english, 2002

33

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

Owen, Ryan P., Gray, Jennifer H., Taylor, Travis R., Carlson, Elaine J., Huang, Conrad C., Kawamoto, Michiko, Johns, Susan J., Stryke, Doug, Ferrin, Thomas E., Giacomini, Kathleen M.

Journal:

Pharmacogenetics and Genomics

Year:

2005

Language:

english

File:

PDF, 251 KB

english, 2005

34

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

Ha Choi, Ji, Wah Yee, Sook, Kim, Mee J., Nguyen, Loan, Ho Lee, Jeong, Kang, Ji-One, Hesselson, Stephanie, Castro, Richard A., Stryke, Doug, Johns, Susan J., Kwok, Pui-Yan, Ferrin, Thomas E., Goo Lee,

Journal:

Pharmacogenetics and Genomics

Year:

2009

Language:

english

File:

PDF, 379 KB

english, 2009

35

[IEEE 2013 IEEE Symposium on Biological Data Visualization (BioVis) - Atlanta, GA, USA (2013.10.13-2013.10.14)] 2013 IEEE Symposium on Biological Data Visualization (BioVis) - Challenge session speakers: Engaging today's genomics resources

Wang, Ting, Ferrin, Thomas

Year:

2013

Language:

english

File:

PDF, 57 KB

english, 2013

36

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

Kroetz, Deanna L, Pauli-Magnus, Christiane, Hodges, Laura M, Huang, Conrad C, Kawamoto, Michiko, Johns, Susan J, Stryke, Doug, Ferrin, Thomas E, DeYoung, Joseph, Taylor, Travis, Carlson, Elaine J, Her

Journal:

Pharmacogenetics

Year:

2003

Language:

english

File:

PDF, 233 KB

english, 2003

37

An Analysis of Frequency, Morphology, and Locations of Maxillary Sinus Septa Using Cone Beam Computed Tomography

Bornstein, Michael, Seiffert, Carol, Maestre-Ferrín, Laura, Fodich, Ivo, Jacobs, Reinhilde, Buser, Daniel, von Arx, Thomas

Journal:

The International Journal of Oral & Maxillofacial Implants

Year:

2016

Language:

english

File:

PDF, 241 KB

english, 2016

38

DASP3: identification of protein sequences belonging to functionally relevant groups

Leuthaeuser, Janelle B., Morris, John H., Harper, Angela F., Ferrin, Thomas E., Babbitt, Patricia C., Fetrow, Jacquelyn S.

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.82 MB

english, 2016

39

UCSF ChimeraX: Meeting Modern Challenges in Visualization and Analysis

Goddard, Thomas D., Huang, Conrad C., Meng, Elaine C., Pettersen, Eric F., Couch, Gregory S., Morris, John H., Ferrin, Thomas E.

Journal:

Protein Science

Year:

2017

Language:

english

File:

PDF, 2.51 MB

english, 2017

40

Molecular Visualization on the Holodeck

Goddard, Thomas D., Brilliant, Alan A., Skillman, Thomas L., Vergenz, Steven, Tyrwhitt-Drake, James, Meng, Elaine C., Ferrin, Thomas E.

Journal:

Journal of Molecular Biology

Year:

2018

Language:

english

File:

PDF, 9.24 MB

english, 2018

41

Anilinoquinoline based inhibitors of trypanosomatid proliferation

Ferrins, Lori, Sharma, Amrita, Thomas, Sarah M., Mehta, Naimee, Erath, Jessey, Tanghe, Scott, Leed, Susan E., Rodriguez, Ana, Mensa-Wilmot, Kojo, Sciotti, Richard J., Gillingwater, Kirsten, Pollastri,

Journal:

PLoS Neglected Tropical Diseases

Year:

2018

Language:

english

File:

PDF, 2.84 MB

english, 2018

42

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

Somboonna, Naraporn, Ziklo, Noa, Ferrin, Thomas E., Hyuk Suh, Jung, Dean, Deborah, Nacy, Carol A.

Journal:

Year:

2019

Language:

english

File:

PDF, 5.72 MB

english, 2019

43

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

Berman, Helen M., Adams, Paul D., Bonvin, Alexandre A., Burley, Stephen K., Carragher, Bridget, Chiu, Wah, DiMaio, Frank, Ferrin, Thomas E., Gabanyi, Margaret J., Goddard, Thomas D., Griffin, Patrick

Journal:

Year:

2019

Language:

english

File:

PDF, 1.69 MB

english, 2019

44

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

Berman, Helen M., Adams, Paul D., Bonvin, Alexandre A., Burley, Stephen K., Carragher, Bridget, Chiu, Wah, DiMaio, Frank, Ferrin, Thomas E., Gabanyi, Margaret J., Goddard, Thomas D., Griffin, Patrick

Journal:

Year:

2019

File:

PDF, 1.69 MB

2019

45

Continued Preoperative Aspirin Use and Bleeding Complications in Patients Undergoing Thyroid Surgery: An Update

Souza, Spenser S., Ferrin, Peter C., Shalaby, Hosam, Abdelgawad, Mohamed, Hoof, Marcus, Hummel, Lena A., Yusin, Thomas M., Raggio, Blake, Ayinapudi, Venkat, Kandil, Emad

Journal:

Journal of the American College of Surgeons

Year:

2019

File:

PDF, 108 KB

2019

46

Reply to Rockey et al., âGenomics and Chlamydial Persistence In Vivo â

Dean, Deborah, Ziklo, Noa, Somboonna, Naraporn, Suh, Jung Hyuk, Ferrin, Thomas

Journal:

Year:

2019

File:

PDF, 163 KB

2019

47

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

Pettersen, Eric F., Goddard, Thomas D., Huang, Conrad C., Meng, Elaine C., Couch, Gregory S., Croll, Tristan I., Morris, John H., Ferrin, Thomas E.

Journal:

Protein Science

Year:

2020

File:

PDF, 5.50 MB

2020

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