kinari.cs.umass.edu

KINARI

KINARI is a suite of tools for calculating and analyzing the rigidity and flexibility of biomolecules, developed in Ileana Streinu. S research group, LinkageLab. To access the KINARI-Web or KINARI-Mutagen tool, select that application's tab and click on the "Access" button. If you use KINARI for research that you publish, please cite:. KINARI-Web: Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu. KINARI-Web: A Server for Protein Rigidity Analysis. 39 (Web Server Issue), 2011. Vol 10, No. 3, 2012.

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KINARI | kinari.cs.umass.edu Reviews

<META> DESCRIPTION

KINARI is a suite of tools for calculating and analyzing the rigidity and flexibility of biomolecules, developed in Ileana Streinu. S research group, LinkageLab. To access the KINARI-Web or KINARI-Mutagen tool, select that application's tab and click on the Access button. If you use KINARI for research that you publish, please cite:. KINARI-Web: Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu. KINARI-Web: A Server for Protein Rigidity Analysis. 39 (Web Server Issue), 2011. Vol 10, No. 3, 2012.

<META> KEYWORDS

1 nucleic acids research

2 kinari web

3 kinari mutagen

4 a quick start

5 generate in silico

6 advanced users

7 video tutorial

8 advanced help

9 see related publications

10 case studies

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nucleic acids research,kinari web,kinari mutagen,a quick start,generate in silico,advanced users,video tutorial,advanced help,see related publications,case studies,and profiling,form

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KINARI | kinari.cs.umass.edu Reviews

https://kinari.cs.umass.edu

KINARI is a suite of tools for calculating and analyzing the rigidity and flexibility of biomolecules, developed in Ileana Streinu. S research group, LinkageLab. To access the KINARI-Web or KINARI-Mutagen tool, select that application's tab and click on the "Access" button. If you use KINARI for research that you publish, please cite:. KINARI-Web: Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu. KINARI-Web: A Server for Protein Rigidity Analysis. 39 (Web Server Issue), 2011. Vol 10, No. 3, 2012.

INTERNAL PAGES

kinari.cs.umass.edu

1

KINARI

http://kinari.cs.umass.edu/Site/casestudies.html

Case Studies Using the KINARI Software. Case studies performed using KINARI-Web. 1HRC - Horse heart cytochrome c. 1HVR - HIV-1 Protease. How a Ligand Affects Protein Rigidity. 2LZM - Bacteriophage T4 Lysozyme. Adding and removing interactions. 4INS, 2HIU, 2TRZ - Pig and Human insulin. Comparing rigidity of structurally similar proteins. Case study performed using KINARI-Mutagen. 2LZM - Lysozyme from bacteriophage T4. 48 Mutant files - A Validation Study. Case studies performed using KINARI-BioUnit.

2

KINARI

http://kinari.cs.umass.edu/Site/publications.html

Click on a title to view abstract.

3

KINARI

http://kinari.cs.umass.edu/Site/profiling.html

Software Profiling and Testing. Two types of software profiling were performed: (1) back-end. Software testing, and (2) front-end. For the front-end testing, each step of KINARI-Web was invoked, including downloading, cleaning/curating a PDB file, performing rigidity analysis, and generating output files necessary to render the protein and the results in the visualizer. Back-End Profile Testing, Composite Results. Click on plot to view full-size pdf version). Curation, 104 residue protein. Number of PDB ...

4

KINARI

http://kinari.cs.umass.edu/Site/requirements.html

KINARI-Web is a web-based application built with html, PHP, Javascript, and the Jmol. Web applet. To run KINARI-Web, you should have Javascript enabled in your browser, and the Java plugin installed. Tested platforms and browsers:. Firefox 3.6.16. Chrome 10.0.647. Firefox 3.6.13. Safari 5.0.3. Firefox 1.0.7. Chrome 4.1.249. Known issues with using KINARI-Web. Firefox 4.0 - With this browser, you might observe one of the known quarks.

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KINARI

http://kinari.cs.umass.edu/Site/feedback.html

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gts2012.tem.uoc.gr

GTS 2012

http://gts2012.tem.uoc.gr/participation.html

Minisymposium on Publicly Available. June 17th and 19th, 2012, Chapel Hill, NC, USA. Book of Abstracts (3.2MB). Minisymposium Program (in PDF). Preparing yourself for participation. Below you may find instructions for installing the software packages for which there will be a tutorial. Dionysus - http:/ www.mrzv.org/software/dionysus. Build Dionysus according to the instructions at http:/ www.mrzv.org/software/dionysus/get-build-install.html. Alternatively, you may follow the steps below:. OGDF - http:/ ...

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KINARI is a suite of tools for calculating and analyzing the rigidity and flexibility of biomolecules, developed in Ileana Streinu. S research group, LinkageLab. To access the KINARI-Web or KINARI-Mutagen tool, select that application's tab and click on the "Access" button. If you use KINARI for research that you publish, please cite:. KINARI-Web: Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu. KINARI-Web: A Server for Protein Rigidity Analysis. 39 (Web Server Issue), 2011. Vol 10, No. 3, 2012.

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