scholarly journals RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design and validation

10.1002/pro.8 ◽  
2008 ◽  
pp. NA-NA ◽  
Author(s):  
Will Sheffler ◽  
David Baker
2020 ◽  
Vol 29 (9) ◽  
pp. 1931-1944
Author(s):  
Alex T. Grigas ◽  
Zhe Mei ◽  
John D. Treado ◽  
Zachary A. Levine ◽  
Lynne Regan ◽  
...  

Author(s):  
M.T. Otten ◽  
P.R. Buseck

ALCHEMI (Atom Location by CHannelling-Enhanced Microanalysis) is a TEM technique for determining site occupancies in single crystals. The method uses the channelling of incident electrons along specific crystallographic planes. This channelling results in enhanced x-ray emission from the atoms on those planes, thereby providing the required site-occupancy information. ALCHEMI has been applied with success to spinel, olivine and feldspar. For the garnets, which form a large group of important minerals and synthetic compounds, the channelling effect is weaker, and significant results are more difficult to obtain. It was found, however, that the channelling effect is pronounced for low-index zone-axis orientations, yielding a method for assessing site occupancies that is rapid and easy to perform.


1970 ◽  
Vol 19 (2) ◽  
pp. 217-226
Author(s):  
S. M. Minhaz Ud-Dean ◽  
Mahdi Muhammad Moosa

Protein structure prediction and evaluation is one of the major fields of computational biology. Estimation of dihedral angle can provide information about the acceptability of both theoretically predicted and experimentally determined structures. Here we report on the sequence specific dihedral angle distribution of high resolution protein structures available in PDB and have developed Sasichandran, a tool for sequence specific dihedral angle prediction and structure evaluation. This tool will allow evaluation of a protein structure in pdb format from the sequence specific distribution of Ramachandran angles. Additionally, it will allow retrieval of the most probable Ramachandran angles for a given sequence along with the sequence specific data. Key words: Torsion angle, φ-ψ distribution, sequence specific ramachandran plot, Ramasekharan, protein structure appraisal D.O.I. 10.3329/ptcb.v19i2.5439 Plant Tissue Cult. & Biotech. 19(2): 217-226, 2009 (December)


2014 ◽  
Vol 3 (5) ◽  
Author(s):  
S. Reiisi ◽  
M. Hashemzade-chaleshtori ◽  
S. Reisi ◽  
H. Shahi ◽  
S. Parchami ◽  
...  

Author(s):  
A.V. Churkov ◽  
◽  
A.A. Rogozin ◽  
V.M. Yatsenko ◽  
T.S. Ignatieva ◽  
...  

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