Automatic Model Building and Verification of Embedded Software with UPPAAL

2011 ◽  
Author(s):  
Xiaoli Gong ◽  
Jie Ma ◽  
Qingcheng Li ◽  
Jin Zhang
Keyword(s):  
Model Building ◽  
Embedded Software ◽  
Automatic Model Building

Automatic model building and solving for optimization problems

1996 ◽  
Vol 18 (1) ◽  
pp. 293-300 ◽  
Author(s):  
J Iijima
Keyword(s):  
Model Building ◽  
Optimization Problems ◽  
Automatic Model Building

Application of constrained real-space refinement of flexible molecular fragments to automatic model building of RNA structures

2012 ◽  
Vol 45 (2) ◽  
pp. 309-315 ◽  
Author(s):  
Frantisek Pavelcik
Keyword(s):  
Nucleic Acid ◽  
Model Building ◽  
Real Space ◽  
Rna Structures ◽  
Molecular Fragments ◽  
Source Codes ◽  
Translation Function ◽  
Base Method ◽  
Nucleic Acid Structures ◽  
Automatic Model Building

New methods have been developed for locating phosphate groups and nucleic acid bases in the electron density of RNA structures. These methods utilize a constrained real-space refinement of molecular fragments and a phased rotation–conformation–translation function. Real-space refinement has also contributed to the improvement of the bone/base method of RNA model building and to redesigning the method of building double helices in nucleic acid structures. This improvement is reflected in the increased accuracy of the model building and the ability to better distinguish between correct and false solutions. A program,RSR, was created, and the programsNUT,HELandDHLwere upgraded and organized into a program system, which is CCP4 oriented. Source codes will also be released.

Protein phasing at non-atomic resolution by combining Patterson andVLDtechniques

2014 ◽  
Vol 70 (7) ◽  
pp. 1994-2006 ◽  
Author(s):  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Giuliana Comunale ◽  
Carmelo Giacovazzo ◽  
...  
Keyword(s):  
Model Building ◽  
Protein Structures ◽  
Experimental Information ◽  
Atomic Resolution ◽  
Data Sets ◽  
Density Maps ◽  
Combined Use ◽  
Final Electron ◽  
Automatic Model Building

Phasing proteins at non-atomic resolution is still a challenge for anyab initiomethod. A variety of algorithms [Patterson deconvolution, superposition techniques, a cross-correlation function (Cmap), theVLD(vive la difference) approach, the FF function, a nonlinear iterative peak-clipping algorithm (SNIP) for defining the background of a map and thefree lunchextrapolation method] have been combined to overcome the lack of experimental information at non-atomic resolution. The method has been applied to a large number of protein diffraction data sets with resolutions varying from atomic to 2.1 Å, with the condition that S or heavier atoms are present in the protein structure. The applications include the use ofARP/wARPto check the quality of the final electron-density maps in an objective way. The results show that resolution is still the maximum obstacle to protein phasing, but also suggest that the solution of protein structures at 2.1 Å resolution is a feasible, even if still an exceptional, task for the combined set of algorithms implemented in the phasing program. The approach described here is more efficient than the previously described procedures:e.g.the combined use of the algorithms mentioned above is frequently able to provide phases of sufficiently high quality to allow automatic model building. The method is implemented in the current version ofSIR2014.

Phased rotation, conformation and translation function: performance with mononucleotides

2008 ◽  
Vol 41 (1) ◽  
pp. 62-67 ◽  
Author(s):  
Frantisek Pavelcik
Keyword(s):  
Nucleic Acid ◽  
Degrees Of Freedom ◽  
Model Building ◽  
Protein Crystallography ◽  
Torsion Angles ◽  
Heavy Atoms ◽  
Promising Tool ◽  
Translation Function ◽  
Nucleic Acid Structures ◽  
Automatic Model Building

A phased rotation, conformation and translation function (PRCTF) is a novel and promising tool for automatic model building in protein crystallography. Its performance has been tested on nucleic acid structures. A mononucleotide fragment of phosphate-to-phosphate type with seven conformation degrees of freedom was used as a search fragment. The position, orientation and internal torsion angles of all localized fragments are refined by a phased flexible refinement. In general, 50 to 93% of the fragments can be found by the PRCTF. Results depend on resolution and phase quality. The ability of the PRCTF to locate bases is significantly lower (3–30%), owing to the lack of heavy atoms. Individual localized fragments can be connected into polynucleotide chains.

scholarly journals Advances in automatic model building and structure completion in the context ofARP/wARP

2008 ◽  
Vol 64 (a1) ◽  
pp. C23-C23 ◽  
Author(s):  
S.X. Cohen ◽  
K. Joosten ◽  
W. Mooij ◽  
V. Lamzin ◽  
G. Murshudov ◽  
...  
Keyword(s):  
Model Building ◽  
Automatic Model Building

scholarly journals Native SAD Structure Solution from Merohedrally Twinned Data

2014 ◽  
Vol 70 (a1) ◽  
pp. C614-C614
Author(s):  
Tobias Weinert ◽  
Sandro Waltersperger ◽  
Vincent Olieric ◽  
Federica Basilico ◽  
Valentina Cecatiello ◽  
...  
Keyword(s):  
Light Source ◽  
Model Building ◽  
Experimental Setup ◽  
Difficult Case ◽  
Space Group ◽  
Human Centromere ◽  
Centromere Protein ◽  
Structure Solution ◽  
Swiss Light Source ◽  
Automatic Model Building

Up until now, comparatively few structures were solved by native SAD. Recent advances in multi crystal averaging [1] have shown that native SAD can be applied to an increasing number of cases. Though theoretically possible [2], successful structure solutions from twinned data have not been reported yet. Here, we report the structure solution of the human Centromere protein M from a merohedrally twinned crystal with a twinning fraction of 0.45 in the space group P3. The data were collected at the bending magnet beamline X06DA at the Swiss Light Source, which is equipped with the in-house developed multi-axis goniometer PRIGo and the PILATUS 2M detector. A highly redundant 2.2 Å dataset was collected in a number of different crystal orientations. A substructure solution could only be obtained after 50000 SHELXD [3] tries. Automatic model building after phasing and density modification resulted in a model with the majority of residues built correctly. We will present this particularly difficult case together with other more routine cases, all solved with the same experimental setup and at the beamline X06DA.

Groupwise Diffeomorphic Non-rigid Registration for Automatic Model Building

2004 ◽  
pp. 316-327 ◽  
Author(s):  
T. F. Cootes ◽  
S. Marsland ◽  
C. J. Twining ◽  
K. Smith ◽  
C. J. Taylor
Keyword(s):  
Model Building ◽  
Rigid Registration ◽  
Automatic Model Building
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