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|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|
C++ compiler, fortran compiler, boost, lapack, CMake
No version available
Publication for PHAISTOS
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.
[…] 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 […]
Taxonomic revision of genus Ablattaria Reitter (Coleoptera, Silphidae) using geometric morphometrics
[…] ♀ (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 […]
ProCS15: a DFT based chemical shift predictor for backbone and Cβ atoms in proteins
[…] ,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 […]
Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics
[…] 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 […]
Reconstruction of SAXS Profiles from Protein Structures
[…] 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 […]
Calculation of accurate small angle X ray scattering curves from coarse grained protein models
[…] 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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