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Enhancing UCSF Chimera through web services
2014
Nucleic Acids Research
Preserved Fulltext
We describe how we have enhanced UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/), a program for the interactive visualization and analysis of molecular structures and related data, through the addition ...
of several web services (http://www.rbvi.ucsf. edu/chimera/docs/webservices.html). ...
services. ...
doi:10.1093/nar/gku377
pmid:24861624
pmcid:PMC4086125
fatcat:jqsigsatobbvrepwsreuwnv6kq
RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps
2014
Bioinformatics
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We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts. ...
We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts. ...
Funding: This work was supported by NIH grant NIGMS P41-GM103311 and the UCSF-Lowell Summer Internship Program. Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/btu841
pmid:25540183
pmcid:PMC4410660
fatcat:aaofce2cfzfojgv5ht6skaf5iy
UCSF Chimera, MODELLER, and IMP: An integrated modeling system
2012
Journal of Structural Biology
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Here we present the integration of several modeling tools into UCSF Chimera. ...
X-ray scattering profiles and fitting of the corresponding experimental profile by IMP FoXS, and assessment of amino acid sidechain conformations based on rotamer probabilities and local interactions by Chimera ...
to the MultiFit web service. ...
doi:10.1016/j.jsb.2011.09.006
pmid:21963794
pmcid:PMC3410985
fatcat:euxgqtlkzvcbvgswfvzulfuo7y
Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians
2020
JMIR Bioinformatics and Biotechnology
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AutoDock Vina (in UCSF [University of California, San Francisco] Chimera) is one of the computationally fastest and most accurate software employed in docking. ...
In this paper, a sequential demonstration of molecular docking of the ligand fisetin with the target protein Akt has been provided, using AutoDock Vina in UCSF Chimera 1.12. ...
Figure 14 . 14 Screenshot of the process to access the Autodock Vina tool in Chimera.
Figure 18 . 18 Selection of the Opal web service app in Chimera. ...
doi:10.2196/14232
fatcat:pcdnvelqlfao7iokl2bgoyyuve
In silico analysis of CDC73 gene revealing 11 novel SNPs with possible association to Hyperparathyroidism-Jaw Tumor syndrome
2020
The EuroBiotech Journal
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Method: Computational analysis using twelve different in-silico tools including SIFT, PROVEAN, PolyPhen-2, SNAP2, PhD-SNP, SNPs&GO, P-Mut, I-Mutant ,Project Hope, Chimera, COSMIC and dbSNP Short Genetic ...
It is available at https://rostlab.org/services/snap2web/.
SNPsGO: Is a web server for predicting disease-associated variations from protein sequence and structure. ...
Illustration was done by UCSF Chimera (v 1.10.2.) and project HOPE. ...
doi:10.2478/ebtj-2020-0008
fatcat:rjvzwnmouvhxzeboo4k2pgve44
cddApp: a Cytoscape app for accessing the NCBI conserved domain database
2014
Computer applications in the biosciences : CABIOS
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., 2011) is a repository of manually curated and computationally derived protein domain family models that are searchable through a Web interface or Web services. ...
If a PDB column was selected as part of the load and a PDB structure was annotated for a node, the Results Panel will also contain a checkbox to open that structure in UCSF Chimera (Pettersen et al., ...
doi:10.1093/bioinformatics/btu605
pmid:25212755
pmcid:PMC4271147
fatcat:2wwumnmptjeqxp4brys6mb2kxi
Identification of novel key biomarkers in Simpson-Golabi-Behmel Syndrome: Evidence from bioinformatics analysis
[article]
2019
bioRxiv
pre-print
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The 3D structure of human GPC3 protein is not available in the Protein Data Bank, so we used RaptorX to generate a 3D structural model for wild-type GPC3 to visualize the amino acids changes by UCSF Chimera ...
Lastly we run conservational analysis by BioEdit and Consurf web server respectively. ...
Combination detection of serum GPC3 and pathogenic SNPs through clinical and genetic testing must be positively matched; this can enhance accuracy and efficiency of hepatocellular carcinoma diagnosis. ...
doi:10.1101/608927
fatcat:7azkqvaogbgmpcxvdey3emplci
In Silico Genetics Revealing 5 Mutations in CEBPA Gene Associated With Acute Myeloid Leukemia
2019
Cancer Informatics
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Chimera tools. ...
The objective of this work was to classify the most deleterious mutation in CCAAT/enhancer-binding protein-alpha ( CEBPA) and to predict their influence on the functional, structural, and expression levels ...
A predicted model was created by RaptorX to visualize and compare the amino acid alterations using UCSF Chimera. 66 UCSF Chimera 1.8 is free for download at http:// www.cgl.ucsf.edu/chimera/. ...
doi:10.1177/1176935119870817
pmid:31621694
pmcid:PMC6777061
fatcat:agdr6c4rw5g4dek27ysjo5h5re
The Dundee Resource for Sequence Analysis and Structure Prediction
2019
Protein Science
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DRSASP resources are available through conventional web interfaces and APIs but are also integrated into the Jalview sequence analysis workbench, which enables the composition of multitool interactive ...
The Dundee Resource for Sequence Analysis and Structure Prediction (DRSASP; http://www.compbio.dundee.ac.uk/drsasp.html) is a collection of web services provided by the Barton Group at the University of ...
Jalview allows quick visualization of these features on a mapped protein structure through its integration with UCSF Chimera. ...
doi:10.1002/pro.3783
pmid:31710725
pmcid:PMC6933851
fatcat:ojsn3m264fhfng7zn5aupfhb5a
Refactoring the Code for Visualizing Protein Database Information in a 3D Viewer for Software Reusability
2008
Genomics & Informatics
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services are frequently just Web APIs that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services. ...
Computer technologies such as Web Services 6 and refactoring are becoming significant in the field of bioinformatics tool development to improve internal consistency and clarity. ...
doi:10.5808/gi.2008.6.1.050
fatcat:5gczmmasezdbjfuydjetc5b2oq
Protein–Protein Modeling Using Cryo-EM Restraints
[chapter]
2020
Msphere
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2020 pre-print arXiv:2005.00435v1 fatcat:kewot5cphralhoo76gqfj7lm5y
Cropping can be straightforwardly performed using UCSF Chimera (Pettersen et al. 2004) . ...
Some of these can be controlled through the web portal interface, for expert tuning of results. ...
doi:10.1007/978-1-0716-0270-6_11
pmid:32006284
fatcat:7mxixdn2jndh3eujigm4w2tj3y
Spring Model – chromatin modeling tool based on OpenMM
[article]
2019
bioRxiv
pre-print
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datasets, studying the impact of structural variants (SVs), inspecting the effects of adding and removing particular contacts, measuring features like maximum distances between certain sites (e.g. promotor-enhancer ...
UCSF Chimera [15] . Additionally the user may download files with restraints saved as 380 a pseudo bonds file format that can be rendered in UCSF Chimera. ...
Web-service:
www.spring-model.cent.uw.edu.pl
Stand-alone
version:
https://bitbucket.org/
4dnucleome/md_soft/
80
author/funder. All rights reserved. ...
doi:10.1101/642322
fatcat:rcz7cvolkneaphcs3dqupjbu5u
SketchBio: a scientist's 3D interface for molecular modeling and animation
2014
BMC Bioinformatics
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Molecular graphics and analyses were performed with the UCSF Chimera package. ...
Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311). ...
Objects can be loaded into SketchBio as .obj files from any program that writes this format or directly through the GUI (via harnessing UCSF Chimera from the PDB or a local .pdb file). ...
doi:10.1186/1471-2105-15-334
pmid:25359079
pmcid:PMC4287593
fatcat:xsxu23n6krfbzdyzy5of76k5ba
SketchBio: A Scientist's 3D Interface for Molecular Modeling and Animation
[article]
2014
arXiv
pre-print
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Molecular graphics and analyses were performed with the UCSF Chimera package. ...
Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311). 3D rendering was performed using ...
Objects can be loaded into SketchBio as .obj files from any program that writes this format or directly through the GUI (via harnessing UCSF Chimera from the PDB or a local .pdb file). ...
arXiv:1407.3145v1
fatcat:cilqxoohc5dm7p52rekahxvnzq
The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes
2017
Journal of Molecular Biology
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To facilitate their use by a broad community, they have been implemented as web portals harvesting both local CPU resources and GPGPU-accelerated EGI grid resources. ...
software packages: PowerFit is a tool for rigid body fitting of atomic structures in cryo-electron density maps and has been updated to also output reliability indicators for the success of fitting, through ...
They can easily be inspected with molecular viewers, such as UCSF Chimera [13] . ...
doi:10.1016/j.jmb.2016.11.032
pmid:27939290
fatcat:i6h2qp5u6bhuhllpye4y2lefba
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