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Protocols

POPSCOMP specifications

Information


Unique identifier OMICS_23949
Name POPSCOMP
Interface Web user interface
Restrictions to use None
Input data A protein structure.
Input format PDB
Computer skills Basic
Maintained No

Publication for POPSCOMP

POPSCOMP citations

 (3)
call_split

Inhibitor induced HER2 HER3 heterodimerisation promotes proliferation through a novel dimer interface

2018
eLife
PMCID: 5929906
PMID: 29712619
DOI: 10.7554/eLife.32271.037
call_split See protocol

[…] 3 into the spaces between atoms.The structural alignment was performed using the multi-seq tool of the VMD 1.9.1 package¬†(), and measurement of interaction surface buried residues was performed using POPScomp¬†(). […]

library_books

Design and application of implicit solvent models in biomolecular simulations

2014
Curr Opin Struct Biol
PMCID: 4045398
PMID: 24841242
DOI: 10.1016/j.sbi.2014.04.003

[…] ximations. An overview of the analysis of protein geometry can be found in Gerstein and Richards []. Fast methods for the SASA computation of proteins and nucleic acids are implemented in POPS [] and POPSCOMP [], a related application for the SASA analysis of biomolecular complexes. Instead of a SASA term, solely the volume of neighbour groups can be used as a measure of desolvation, as in the EEF […]

call_split

Structure and Stability Insights into Tumour Suppressor p53 Evolutionary Related Proteins

2013
PLoS One
PMCID: 3790848
PMID: 24124530
DOI: 10.1371/journal.pone.0076014
call_split See protocol

[…] surface areas (SASA) were computed using the POPS software [,] and interface residues were determined as the residues that show a 10% reduced SASA compared to the fully exposed state calculated with POPSCOMP []. The probability of an amino acid involved in an interface is given by p = (number of occurrences of amino acids located at an interface / number of instances of the amino acids). […]

Citations

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POPSCOMP institution(s)
Bioinformatics Unit, Faculty of Sciences, Vrije Universiteit, De Boelelaan, Amsterdam, The Netherlands; Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, London, UK

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