Top 10 similar words or synonyms for molprobity

procheck    0.762424

laskowski    0.758305

refmac    0.692561

krissinel    0.675743

xtalview    0.669424

shelxl    0.655282

yasara    0.644177

sheldrick    0.641682

murshudov    0.636018

luthy    0.635037

Top 30 analogous words or synonyms for molprobity

Article Example
Jane S. Richardson The Richardsons' more recent work has diversified beyond classification and crystallography. In the 1980s they stretched into the fields of synthetic biochemistry and computational biology as pioneers in the de novo design of proteins. In the 1990s they developed the kinemage system of molecular graphics and David wrote the Mage program to display them on small computers, for the then-new journal Protein Science, and they developed all-atom contact analysis (see image) to measure "goodness of fit" inside proteins and in interactions with surrounding molecules. The Richardson Laboratory currently studies structural motifs in RNA as well as proteins, as part of the RNA Ontology Consortium (ROC), acted as assessors in the CASP8 structure-prediction experiment (CASP), is one of the four developer teams on the PHENIX software system for x-ray crystallography of macromolecules, and hosts the MolProbity web service for validation and accuracy improvement of protein and RNA crystal structures. MolProbity uses the KiNG program (successor to Mage) for showing 3D kinemage graphics on-line. Jane serves on the worldwide Protein Data Bank (wwPDB) X-ray Validation Task Force and NMR Validation Task Force.
Resolution by Proxy Over the past 20 years several methods have been proposed to calculate “equivalent resolution” using only X-ray coordinate data (rather than X-ray diffraction data). Some were designed specifically for evaluating NMR structures such as Procheck-NMR while others were designed more for structure quality evaluation and validation of X-ray structures such as MolProbity, and RosettaHoles2. However, these methods rely on a relatively small number of protein structure quality measures to predict resolution (4, 3, and 1 measures, respectively) and consequently the correlation between observed (X-ray) resolution and the predicted resolution is not particularly good. By expanding the number of structure features to include the distribution of torsion angles, the presence of atom clashes, the normality of hydrogen bonding, the numbers of violations of bond lengths and bond angles, the presence of cavities, residue-specific packing volumes, packing efficiency and threading energies it is possible to improve this correlation quite substantially.
Sorbitol dehydrogenase The structure of human sorbitol dehydrogenase was determined through crystallization experiments and X-ray diffraction (with a resolution of 2.20 Å). The method used for crystallization was “Vapor Diffusion, Hanging Drop” at pH 6.2 and at a temperature of 295.0 K. Sorbitol dehydrogenase consists of four identical chains (A, B, C, D), each of which being 31% helical (14 helices) and 26% beta sheet (23 strands). MolProbity Ramachandran analysis was conducted by Lovell, Davis, et al. The results were that 97.1% of all residues were in favored regions and 100.0% of all residues were in allowed regions, with no outliers. All four chains have 356 residues each and a catalytic site. The catalytic sites contain both a serine and a histidine residue, which are hydrophilic sidechains. The residues require NAD+ and a zinc ion to be present for catalytic activity. Sorbitol dehydrogenase belongs to the oxidoreductase family, which means that it helps catalyze oxidation reduction reactions. As stated above, the enzyme helps in the pathway of converting glucose into fructose.
Resolution by Proxy ResProx uses a collection of 25 different protein structure features (such as torsion angle distributions, hydrogen bonding, packing volume, cavities, Molprobity measures) that were used in a Support Vector Regression method to maximize the correlation between the predicted resolution and the observed X-ray resolution on a set of 2400 protein structures with known X-ray resolution. The exact details of the algorithm are provided in a paper published by Dr. Wishart and colleagues. After training and appropriate validation on independent tests sets, this SVR model is able to estimate the resolution of solved X-ray structures with a correlation coefficient of 0.92, mean absolute error of 0.28 Angstroms. This is about 15-30% better than existing methods. This is shown in Figure 1. Because the performance of the ResProx method is so high and because it only needs coordinate data to generate an estimate of the equivalent X-ray resolution, it is ideally suited to be applied to NMR structures. Interestingly when NMR structures are analyzed by ResProx, the average NMR structure has an equivalent X-ray resolution of 2.8 Angstroms—which is relatively poor (Fig. 2). This is in agreement with qualitative observations regarding the overall quality and precision of NMR structures. As seen in Figure 2, a very small number NMR structures exhibit a resolution equivalent to < 1.0 Angstroms—but these are rare.
Fibroblast growth factor receptor 1 The phosphorylation of tyrosine 653 and tyrosine 654 in the active kinase conformation causes a large conformation change in the activation segment of FGFR1 kinase. Threonine 658 is moved by 24Å from the inactive form (Figure 3.) to the activated form of FGFR1 kinase (Figure 4.). The movement causes the closed conformation in the inactive form to open to enable substrate binding. It also allows the open conformation to coordinate Mg2+ with AMP-PCP (analog of ATP). In addition, pY653 and pY654 in the active form helps to maintain the open conformation of the SH2 and FGFR1 kinase complex. However, the mechanism of which the phosphorylation at Y653 and Y654 helps to recruit SH2 domain to its C-terminal tail upon phosphorylation of Y766 remains elusive. Figure 5 shows the overlay structure of active and inactive forms of FGFR1 kinase. Figure 6 shows the dots and contacts on phosphorylated tyrosine residues 653 and 654. Green dots show highly favorable contacts between pY653 and pY654 with surrounding residues. Red spikes show unfavorable contacts in the activation segment. The figure is generated through Molprobity extension on Pymol.