SphereGrinder statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SphereGrinder
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Tool usage distribution map

This map represents all the scientific publications referring to SphereGrinder per scientific context
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Associated diseases

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Protocols

SphereGrinder specifications

Information


Unique identifier OMICS_16761
Name SphereGrinder
Software type Framework/Library
Interface Graphical user interface
Input data A reference structure and some predicted models.
Input format PDB
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Requirements
OpenGL
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Piotr Lukasiak

Additional information


http://spheregrinder.cs.put.poznan.pl/index.php?slab=help http://spheregrinder.cs.put.poznan.pl/index.php?slab=about

Publication for SphereGrinder

SphereGrinder citations

 (2)
library_books

FF12MC: A revised AMBER forcefield and new protein simulation protocol

2016
Proteins
PMCID: 5129589
PMID: 27348292
DOI: 10.1002/prot.25094

[…] , and GDT‐TS were also included in the present study. While sseRMSD, CαRMSD, GDT‐TS, GDT‐HA, and GDC‐all are five QSs based on global alignment, RPF and LDDT are two QSs based on local alignment. The SphereGrinder score and the CAD score were therefore included to balance the local‐alignment scores with the global‐alignment scores. Hereafter, RPF9 and LDDT15 denote the RPF and LDDT scores that wer […]

call_split

Evaluation of predictions in the CASP10 model refinement category

2014
Proteins
PMCID: 4282348
PMID: 23900810
DOI: 10.1002/prot.24377
call_split See protocol

[…] lation and its choice is amino-acid-dependent. In this case, the cd values come from 10 different alignments of the target and the model with distance thresholds of 0.5, 1.0, 1.5, … 4.0, 4.5, and 5 Å.SphereGrinder (SphGr) score, which is calculated from local comparisons of predicted and observed atomic coordinate subsets. For each residue in the target structure, all atoms within 6 Å of its Cα in […]


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SphereGrinder institution(s)
Institute of Computing Science, Poznan University of Technology, Poznan, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Protein Structure Prediction Center, Genome and Biomedical Sciences Facility, University of California, Davis, CA, USA
SphereGrinder funding source(s)
Supported by National Science Center Poland [2012/05/B/ST6/03026], National Science Center Poland [2012/061 A/ST6/00384].

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