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PHAISTOS specifications

Information


Unique identifier OMICS_13889
Name PHAISTOS
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Beta
Requirements
C++ compiler, fortran compiler, boost, lapack, CMake
Maintained Yes

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Publication for PHAISTOS

PHAISTOS citations

 (6)
call_split

Protein structure refinement using a quantum mechanics based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.

2016
PMCID: 5399634
PMID: 28451325
DOI: 10.1039/c6sc04344e
call_split See protocol

[…] nce criterion of 0.01 kcal mol–1 Å–1.The CHARMM/CMAP energy minimized structures were used as starting points for two different kinds of Markov Chain Monte Carlo (MCMC) simulations, carried out using PHAISTOS with the Metropolis–Hastings acceptance criterion using the hybrid energy function described above: simulated annealing, and constant temperature simulations. The physical force field CHARMM3 […]

library_books

Taxonomic revision of genus Ablattaria Reitter (Coleoptera, Silphidae) using geometric morphometrics

2015
Zookeys
PMCID: 4319058
PMID: 25685005
DOI: 10.3897/zookeys.477.8446

[…] ♀ (SMNS); Mitass, Epar. Kanurgion [not located], 16.v.1925, A. Schulz leg., 1 ♀ (ZMHB); Crete, 1884, Oertzen leg., 1 ♀ (NHMW), same locality, Viano [Viannos], without date, Oertzen leg., 1 ♀ (ZMHB); Phaistos, iii.1981, Schurmann leg., 1 ♀ (SMNS); Rethimnon, 14.iv.1980, Korell leg., 1 ♂, 2 ♀ (JRUC); same locality, Melambes (15 km South-East Spili), 35°08'N 24°39'E, 200 m, 7.v.1995, C. Lange & J. Z […]

library_books

ProCS15: a DFT based chemical shift predictor for backbone and Cβ atoms in proteins

2015
PeerJ
PMCID: 4662583
PMID: 26623185
DOI: 10.7717/peerj.1344

[…] ,p)//PM6-D3H+ GIAO NMR shielding calculations were performed with Gaussian09 using the CPCM solvation model. ProCS15 calculations were done using a module written for the protein simulation framework PHAISTOS (). The module was specifically written for this paper and can be downloaded at github.com/jensengroup/procs15. CheShift-2 calculations were performed using either the web interface at cheshi […]

library_books

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

2013
PLoS One
PMCID: 3877219
PMID: 24391900
DOI: 10.1371/journal.pone.0084123

[…] ed on the OPLS energy function. The latter brings in the experimental data, and is based on the difference between the back-calculated data from a simulated structure and the experimental data. Using PHAISTOS, we draw samples from the joint probability distribution, which is given by:(5)where represents a protein structure, is experimental chemical shift data and denotes prior information, such […]

library_books

Reconstruction of SAXS Profiles from Protein Structures

2013
Comput Struct Biotechnol J
PMCID: 3962079
PMID: 24688746
DOI: 10.5936/csbj.201308006

[…] In 2012, the SAXS algorithm in PHAISTOS was accelerated using general purpose graphical processing units (GPGPUs)[]. This method utilizes Bayesian probability statistics to compute the form factors in the Debye equation for protein […]

library_books

Calculation of accurate small angle X ray scattering curves from coarse grained protein models

2010
BMC Bioinformatics
PMCID: 2931518
PMID: 20718956
DOI: 10.1186/1471-2105-11-429

[…] that surrounds the protein [] and a probabilistic description of the experimental errors associated with a SAXS data acquisition experiment [,]. We are currently implementing such an approach in the PHAISTOS software package [,]. […]

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PHAISTOS institution(s)
Department of Biology, University of Copenhagen, Copenhagen, Denmark; Department of Astronomy and Theoretical Physics, University of Lund, Lund, Sweden; Center for Bioinformatics, University of Hamburg, Hamburg, Germany; Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy; Department of Biomedical Engineering, DTU Elektro, DTU, Kongens Lyngby, Denmark; Institute, University of Copenhagen, Copenhagen, Denmark; Computational Biology Unit, Uni Computing, Uni Research, Norway; Department of Chemistry, University of Copenhagen, Copenhagen, Denmark; BILS, Science for Life Laboratory, Box 1031, Solna, Sweden
PHAISTOS funding source(s)
This work was supported by Danish Council for Independent Research (FNU272-08-0315, FTP274-06-0380, FTP09–066546 and FTP274-08-0124), Danish Council for Strategic Research (NABIIT2106-06-0009), Novo Nordisk STAR Program, Novo Nordisk Foundation, and Radiometer (DTU).

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