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Enhancing UCSF Chimera through web services

Conrad C. Huang, Elaine C. Meng, John H. Morris, Eric F. Pettersen, Thomas E. Ferrin
2014 Nucleic Acids Research  
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

J. E. Chen, C. C. Huang, T. E. Ferrin
2014 Bioinformatics  
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

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
2012 Journal of Structural Biology  
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

Sania Safdar Butt, Yasmin Badshah, Maria Shabbir, Mehak Rafiq
2020 JMIR Bioinformatics and Biotechnology  
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

Abdelrahman H. Abdelmoneim, Alaa I. Mohammed, Esraa O. Gadim, Mayada Alhibir Mohammed, Sara H. Hamza, Sara A. Mirghani, Thwayba A. Mahmoud, Mohamed A. Hassan
2020 The EuroBiotech Journal  
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

John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin
2014 Computer applications in the biosciences : CABIOS  
., 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]

Mujahed I. Mustafa, Abdelrahman H. Abdelmoneim, Nafisa M. Elfadol, Naseem S. Murshed, Zainab O. Mohammed, Mohamed A. Hassan
2019 bioRxiv   pre-print
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

Mujahed I Mustafa, Zainab O Mohammed, Naseem S Murshed, Nafisa M Elfadol, Abdelrahman H Abdelmoneim, Mohamed A Hassan
2019 Cancer Informatics  
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

Stuart A. MacGowan, Fábio Madeira, Thiago Britto‐Borges, Mateusz Warowny, Alexey Drozdetskiy, James B. Procter, Geoffrey J. Barton
2019 Protein Science  
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

Yoo-Jin Chun, Seong-Il Ham, San-Duk Yang, Arang Rhie, Hyun-Seok Park
2008 Genomics & Informatics  
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]

Mikael Trellet, Gydo van Zundert, Alexandre M. J. J. Bonvin
2020 Msphere  
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]

Michal Kadlof, Julia Rozycka, Dariusz Plewczynski
2019 bioRxiv   pre-print
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

Shawn M Waldon, Peter M Thompson, Patrick J Hahn, Russell M
2014 BMC Bioinformatics  
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]

Shawn M. Waldon, Peter M. Thompson, Patrick J. Hahn, Russell M. Taylor II
2014 arXiv   pre-print
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

G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato, A.M.J.J. Bonvin
2017 Journal of Molecular Biology  
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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