How to Install and Uninstall concavity Package on Ubuntu 16.04 LTS (Xenial Xerus)

Last updated: May 15,2024

1. Install "concavity" package

Please follow the guidance below to install concavity on Ubuntu 16.04 LTS (Xenial Xerus)


    
        
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                sudo apt update
            
                    
    
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                sudo apt install
            
                        
                concavity
            
                    
    
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2. Uninstall "concavity" package

This is a short guide on how to uninstall concavity on Ubuntu 16.04 LTS (Xenial Xerus):


    
        
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                sudo apt remove
            
                        
                concavity
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the concavity package on Ubuntu 16.04 LTS (Xenial Xerus)

Package: concavity
Priority: extra
Section: universe/science
Installed-Size: 549
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Architecture: amd64
Version: 0.1+dfsg-1
Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 4.1.1)
Suggests: conservation-code, pymol
Filename: pool/universe/c/concavity/concavity_0.1+dfsg-1_amd64.deb
Size: 285650
MD5sum: 81674ae292cb7b61d07ea562905cec6b
SHA1: d92b05ab65c6149aee885755fc31163724442c58
SHA256: 81e82fa6568907c6eef77a36c7c24cde21721ee36aaebc3d7652f0db60f8d1b9
Description-en: predictor of protein ligand binding sites from structure and conservation
ConCavity predicts protein ligand binding sites by combining evolutionary
sequence conservation and 3D structure.
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ConCavity takes as input a PDB format protein structure and optionally
files that characterize the evolutionary sequence conservation of the chains
in the structure file.
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The following result files are produced by default:
* Residue ligand binding predictions for each chain (*.scores).
* Residue ligand binding predictions in a PDB format file (residue
scores placed in the temp. factor field, *_residue.pdb).
* Pocket prediction locations in a DX format file (*.dx).
* PyMOL script to visualize the predictions (*.pml).
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ConCavity has many features. The default run of concavity is equivalent to
ConCavity in the paper:
'Capra JA, Laskowski RA, Thornton JM, Singh M, and Funkhouser TA(2009)
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence
Conservation and 3D Structure. PLoS Comput Biol, 5(12).'.
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score_conservation(1) from the conservation-code package can be used to
calculate evolutionary sequence conservation for concavity.
Description-md5: 41a7ba016e46612a41930328ca6837c2
Homepage: http://compbio.cs.princeton.edu/concavity/
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Origin: Ubuntu