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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
2004 Journal of Computational Chemistry  
The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed.  ...  Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera  ...  Acknowledgments We thank David Konerding and Joe Murray for their contributions to early versions of Chimera. We would also like to thank Patricia  ... 
doi:10.1002/jcc.20084 pmid:15264254 fatcat:f7kzbqy7cve5rg7wmzoty2xoty

Caloinophyllin A, a new chromanone derivative from Calophyllum inophyllum roots

Sasa Ponguschariyagul, Jirapast Sichaem, Suttira Khumkratok, Pongpun Siripong, Kiattisak Lugsanangarm, Santi Tip-Pyang
2018 Figshare  
Moreover, all isolated compounds were assessed for their in vitro cytotoxicity against five human cancer cell lines.  ...  A new chromanone derivative, namely caloinophyllin A (1), along with eight known compounds (2–9), nobiletin (2), pentamethylquercetin (3), 3,5,7,4′-tetramethoxyflavone (4), 5,7,4′-trimethoxyflavone (5)  ...  Greenblatt DM, Meng EC and Ferrin TE. (2004) UCSF Chimera-A visualization system for exploratory research and analysis.  ... 
doi:10.6084/m9.figshare.5802774 fatcat:xfgydn7syfgn5oxstmk5k4vw7y

Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins

Samuel Hertig, Thomas D. Goddard, Graham T. Johnson, Thomas E. Ferrin
2015 Biophysical Journal  
MDA automates the tasks of template searching, visualization, and selection followed by multidomain model generation, and is part of the widely used molecular graphics package UCSF CHIMERA (University  ...  regions have a few distant homologs.  ...  MDA modeling is performed in the three-dimensional visualization package UCSF CHIMERA, providing rich structural information on templates.  ... 
doi:10.1016/j.bpj.2015.03.051 pmid:25954868 pmcid:PMC4423039 fatcat:wuxqcjjbbzhqbinffgqlbwnjxe

Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding

Rebecca Beveridge, Lukasz G. Migas, Karl A. P. Payne, Nigel S. Scrutton, David Leys, Perdita E. Barran
2016 Nature Communications  
For further methodological details see main text, protein images made using UCSF Chimera 1 .  ...  a) Collision Cross Section (calculated using the 'Exact Hard Sphere' method) vs time.  ...  = 200V (harsh), and b) cone voltage = 60 V (softer).  ... 
doi:10.1038/ncomms12163 pmid:27418477 pmcid:PMC4947166 fatcat:iclbdeqgafaf5asi6uzcaz4hkq

The Effect of Structural Modification on the Blood Brain Barrier Permeation Properties of Allicin

Victor E. Itepu, Ogochukwu J. Umezinwa, Fidelis A. Ilukho, Difa A. Collins, Cosmas Samuel
2019 Asian Journal of Research in Biochemistry  
It is also sourced from onions, and different species in the family Alliaceae. It was first isolated and examined in the research facility by Chester J. Cavallito in 1944.  ...  This colourless fluid has a distinctively pungent smell. This compound shows antibacterial and anti-fungal properties.  ...  UCSF Chimera--A visualization system for exploratory research and analysis. J Computational Chemistry. 2004;25(13):1605-1612. 21.  ... 
doi:10.9734/ajrb/2019/v5i330092 fatcat:3idzuwxrm5fhtk4vya2lnilbca

In-Silico Study of Neural Tube Defect in Relation to FOHL1 Gene

Barkha Singh Barkha Singh, Rashmi Rashmi, Sunil Kumar Rai, Sangeeta Rai, Royana Singh Royana Singh
2012 International Journal of Scientific Research  
The study helps in determining new insight for the genetic analysis of FOLH1 gene with neural tube defect.  ...  A total of 1778 SNPs are investigated for FOLH1. Bioinformatics tools were used to determine SNP (rs61886492).  ...  ,C., Ferrin T., E., (2004) UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry; 25 (13), 1605-1612. | 20. Yuan, H.  ... 
doi:10.15373/22778179/apr2014/130 fatcat:qbfeqavm2ngt3d2swmjek35ebq

Page 236 of Cellular and Molecular Life Sciences Vol. 65, Issue 2 [page]

2008 Cellular and Molecular Life Sciences  
C. and Ferrin, T. E. (2004) UCSF chimera — Avisualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612. To access this journal online: http ://www.birkhauser.ch/CMLS  ...  C. and Ferrin, T. E. (2007) Visualizing density maps with UCSF Chimera. J. Struc. Biol. 157, 281-287. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E.  ... 

Page 999 of Genetics Vol. 170, Issue 3 [page]

2005 Genetics  
GREENBLATT ef al., 2004 UCSF Chimeraa visualization system for exploratory research and analysis. ]. Comput. Chem. 25: 1605- 1612 Poon, A., B. H. Davis and L.  ...  CHEN and B. A. FANrE, 2004 Genetic and functional analysis of the 9X174 DNA binding protein: the effects of substitutions for amino acid residues that spatially organize the two DNA binding domains.  ... 

An In Silico Approach for Characterization of an Acetyltransfarase Protein from Shigella flexneri Serotype 5b (strain 8401)

2017 Journal of Proteomics & Computational Biology  
A hypothetical protein yjaB of these bacteria, consisting of 147 residues was picked out for in silico analysis.  ...  Sequence similarity was brought in through Protein Data Bank and non-redundant database using BLASTp program of NCBI and a search for templates revealed that yjaB shares 97% homology to a protein of Escherichia  ...  Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF chimera--a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612. 29.  ... 
doi:10.13188/2572-8679.1000007 fatcat:pmqois37cbh7lfyzfzp6c7quxq

Page 1310 of Cellular and Molecular Life Sciences Vol. 65, Issue 9 [page]

2008 Cellular and Molecular Life Sciences  
C. and Ferrin, T. E. (2004) UCSF ChimeraA visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612 To access this journal online: http ://www.birkhauser.ch/CMLS  ...  Zelensky, A. N. and Gready, J. E. (2003) Comparative analysis of structural properties of the C-type-lectin-like domain (CTLD). Proteins 52, 466-477.  ... 

Computational Tools for the Interactive Exploration of Proteomic and Structural Data

John H. Morris, Elaine C. Meng, Thomas E. Ferrin
2010 Molecular & Cellular Proteomics  
We briefly describe several relevant tools, and then, using three scenarios, we present in depth two tools for the integrated  ...  Linking proteomics and structural data is critical to our understanding of cellular processes, and interactive exploration of these complementary data sets can be extremely valuable for developing or confirming  ...  A number of visualization and analysis tools are used for protein networks.  ... 
doi:10.1074/mcp.r000007-mcp201 pmid:20525940 pmcid:PMC2938059 fatcat:x3yridoahfeq5gooebinxhmtby

Macromolecular Assemblies Highlighted

Andrej Sali, Wah Chiu
2005 Structure  
This special issue of Structure sembly as well as suggest mechanistic models of its focuses on the methods for characterization, analysis, function. visualization and annotation of the structures of com-Keiichi  ...  Specifically, both compupanded the applicability of existing methods to integtational and visualization methods for analysis of the rate structural information gathered at multiple levels electron-cryomicroscopy  ...  More-even at very high-compression ratios, which allows for efficient exploratory visualization of the macromolecu-over, a few dominant modes of motion are sufficient to describe the anisotropic expansion  ... 
doi:10.1016/j.str.2005.02.010 fatcat:xiaqhrsskva3rb4giywlgy24wq

Structural insight into Pichia pastoris fatty acid synthase [article]

Joseph S Snowden, Jehad Alzahrani, Lee Sherry, Martin Stacey, David J Rowlands, Neil A Ranson, Nicola J Stonehouse
2021 bioRxiv   pre-print
Serendipitously, we identified FAS as a contaminant in a cryoEM dataset of virus-like particles (VLPs) purified from P. pastoris, an important model organism and common expression system used in protein  ...  Ultimately, the structure reported here will be a useful resource for further efforts to engineer yeast FAS for synthesis of alternate products.  ...  UCSF Chimera -a visualization system for exploratory research  ... 
doi:10.1101/2021.01.27.428426 fatcat:qkg5xmuqlfeq7k3k2xlhqsuu4e

Insights into the structure of the CCR4-NOT complex by electron microscopy

Fariborz Nasertorabi, Claire Batisse, Meikel Diepholz, Dietrich Suck, Bettina Böttcher
2011 FEBS Letters  
The UCSF Chimera package originates from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR-01081).  ...  Part of the work was carried out in the Electron Cryo Microscopy facility at the University of Edinburgh (supported by the Scottish Alliance for Life Sciences and the Wellcome Trust, WT087658MA).  ...  UCSF Chimera-a visualization system for exploratory research and analysis. J. Biochemical characterization of the purification of the CCR4-NOT complex .  ... 
doi:10.1016/j.febslet.2011.05.071 pmid:21669201 pmcid:PMC3171648 fatcat:3jgzhup22vbx7o6pglvdxlawum

Page 8 of Cellular and Molecular Life Sciences Vol. 63, Issue 2 [page]

2006 Cellular and Molecular Life Sciences  
C. et al. (2004) UCSF Chimeraa visualization system for exploratory research and analysis. J. Comput. Chem. 25: 1605-1612 Sanner M. F., Olson A. J. and Spehner J.  ...  Cancer. 17: 565-577 Larsson R. and Nygren P. (1989) A rapid fluorometric method for semiautomated determination of cytotoxicity and cellular proliferation of human tumor cell lines in microculture.  ... 
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