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AlloPred specifications

Information


Unique identifier OMICS_10323
Name AlloPred
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data PDB ID and chain(s) or PDB file
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
Python, Numpy, Prody, fpocket, SVM-light
Maintained Yes

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Maintainer


  • person_outline Joe G. Greener <>

Information


Unique identifier OMICS_10323
Name AlloPred
Interface Web user interface
Restrictions to use None
Input data PDB ID and chain(s) or PDB file
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Joe G. Greener <>

Publication for AlloPred

AlloPred citations

 (2)
library_books

A computational study for rational HIV 1 non nucleoside reverse transcriptase inhibitor selection and the discovery of novel allosteric pockets for inhibitor design

2018
PMCID: 5835713
PMID: 29437904
DOI: 10.1042/BSR20171113

[…] overall and had the highest ‘druggability’ score in the top five identified pockets (see supplementary figure s1). we then independently performed allosteric pocket prediction for pdb:3t19 on the allopred server [] (refer to greener and sternberg [] for more details), and found that four out of five identified pockets above were predicted to be ‘allosteric’ (with the known nnrti-binding […]

library_books

Predicting Protein Dynamics and Allostery Using Multi Protein Atomic Distance Constraints

2017
PMCID: 5343748
PMID: 28190781
DOI: 10.1016/j.str.2017.01.008

[…] () is an implementation of the earlier binding leverage algorithm (), which models how perturbations due to binding couple to the motions of the protein as expressed by low-frequency normal modes. allopred () uses perturbation of normal modes and pocket features in a machine-learning approach to predict allosteric pockets. it should be noted that different criteria are used to define […]


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AlloPred institution(s)
Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK

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