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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 in publications

 (10)
PMCID: 5319673
PMID: 28222134
DOI: 10.1371/journal.pone.0170727

[…] insights into the processes shaping landscapes. this work examines the influence of landform classification on the settlement locations of bronze age (minoan) crete, focusing on the districts of phaistos, kavousi and vrokastro. the landform classification was based on the topographic position index (tpi) and deviation from mean elevation (dev) analysis to highlight slope steepness of various […]

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 & […]

PMCID: 4375973
PMID: 25825683
DOI: 10.7717/peerj.861

[…] \end{eqnarray*}\end{document}ehybridx,θ=−kbtlnpx,θ∣d=kbt∑jnj+1lnγj+∑i=1njln1+δδijγj2+ex., markov chain monte carlo simulations were carried out with phaistos v1.0 () using either the multicanonical generalized ensemble via muninn () or metropolis–hastings (). chemical shift predictions were performed with an implementation of camshift () […]

PMCID: 3958820
PMID: 24469314
DOI: 10.3390/ijms15021767

[…] of ubiquitin and other proteins more efficiently than the cra move set []. the crisp move along with cra, crankshaft, pivot, and other mc move sets has been implemented in a program suite called “phaistos” for rapid conformational sampling of proteins in implicit solvents []., we have recently presented a very different local-move set mc method, the chain breakage/closure (cbc) algorithm, […]

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

[…] is parameterized against quantum mechanical (qm) calculations and reproduces high level qm results obtained for a small protein with an rmsd of 0.25 ppm (r = 0.94). procs is interfaced with the phaistos protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. such chemical shift-based structural […]


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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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