scholarly journals Completion of autobuilt protein models using a database of protein fragments

2012 ◽  
Vol 68 (4) ◽  
pp. 328-335 ◽  
Author(s):  
Kevin Cowtan
Keyword(s):  
Model Building ◽  
General Purpose ◽  
Search Method ◽  
Model Completeness ◽  
Protein Fragments ◽  
Arbitrary Size ◽  
Protein Model ◽  
Protein Models

Two developments in the process of automated protein model building in the Buccaneer software are presented. A general-purpose library for protein fragments of arbitrary size is described, with a highly optimized search method allowing the use of a larger database than in previous work. The problem of assembling an autobuilt model into complete chains is discussed. This involves the assembly of disconnected chain fragments into complete molecules and the use of the database of protein fragments in improving the model completeness. Assembly of fragments into molecules is a standard step in existing model-building software, but the methods have not received detailed discussion in the literature.

scholarly journals The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution

2020 ◽  
Vol 76 (3) ◽  
pp. 248-260 ◽  
Author(s):  
Grzegorz Chojnowski ◽  
Koushik Choudhury ◽  
Philipp Heuser ◽  
Egor Sobolev ◽  
Joana Pereira ◽  
...  
Keyword(s):  
Model Building ◽  
Structural Information ◽  
Structural Similarity ◽  
Molecular Replacement ◽  
Sequence Coverage ◽  
Protein Model ◽  
Model Extension ◽  
Replacement Solution ◽  
Almost All ◽  
Protein Models

The performance of automated protein model building usually decreases with resolution, mainly owing to the lower information content of the experimental data. This calls for a more elaborate use of the available structural information about macromolecules. Here, a new method is presented that uses structural homologues to improve the quality of protein models automatically constructed using ARP/wARP. The method uses local structural similarity between deposited models and the model being built, and results in longer main-chain fragments that in turn can be more reliably docked to the protein sequence. The application of the homology-based model extension method to the example of a CFA synthase at 2.7 Å resolution resulted in a more complete model with almost all of the residues correctly built and docked to the sequence. The method was also evaluated on 1493 molecular-replacement solutions at a resolution of 4.0 Å and better that were submitted to the ARP/wARP web service for model building. A significant improvement in the completeness and sequence coverage of the built models has been observed.

scholarly journals Sequence assignment for low-resolution modelling of protein crystal structures

2019 ◽  
Vol 75 (8) ◽  
pp. 753-763 ◽  
Author(s):  
Grzegorz Chojnowski ◽  
Joana Pereira ◽  
Victor S. Lamzin
Keyword(s):  
Model Building ◽  
Protein Crystal ◽  
Side Chain ◽  
Sequence Coverage ◽  
Protein Fragments ◽  
New Methods ◽  
Combined Use ◽  
Protein Models ◽  
Automated Model Building ◽  
Sequence Assignment

The performance of automated model building in crystal structure determination usually decreases with the resolution of the experimental data, and may result in fragmented models and incorrect side-chain assignment. Presented here are new methods for machine-learning-based docking of main-chain fragments to the sequence and for their sequence-independent connection using a dedicated library of protein fragments. The combined use of these new methods noticeably increases sequence coverage and reduces fragmentation of the protein models automatically built with ARP/wARP.

Cyclic Performance of Two-Story Ductile RC Frames With Infill Walls

2005 ◽  
Author(s):  
Yung-Hsin Yeh ◽  
Wen-I Liao
Keyword(s):  
Model Building ◽  
General Purpose ◽  
Rc Frame ◽  
Building Structures ◽  
Base Shear ◽  
Concrete Frames ◽  
Infill Wall ◽  
Infill Walls ◽  
Rc Frames ◽  
Short Beam

This paper presents the results of the experimental and analytical investigations conducted on four 0.8 scale 2-story one bay ductile reinforced concrete frames with infill nonstructural walls subjected to cyclically increasing loads. The material properties and the member sizes of beams and columns in the four RC frame specimens are identical, but with different types of infill nonstructural wall. These four frames are the pure frame, frame with short column, frame with short beam and frame with wing walls. The four RC frame specimens were designed and constructed according to the general prototype building structures in Taiwan. Test results indicate that the ductility behavior of the frames with infill wall is similar to those of the pure frame. The ultimate base shear strength of the frames with infill walls is higher than those of the pure frame. Analytical results show that the proposed simplified multi-linear beam-column element implemented in a general purpose structural analysis program can accurately simulate the cyclic responses of the RC frame specimen incorporating the elastic flexural stiffness computations suggested by the model building codes.

scholarly journals Cryo‐EM map interpretation and protein model‐building using iterative map segmentation

2019 ◽  
Vol 29 (1) ◽  
pp. 87-99 ◽  
Author(s):  
Thomas C. Terwilliger ◽  
Paul D. Adams ◽  
Pavel V. Afonine ◽  
Oleg V. Sobolev
Keyword(s):  
Model Building ◽  
Map Interpretation ◽  
Protein Model ◽  
Map Segmentation

scholarly journals Fast structure similarity searches among protein models: efficient clustering of protein fragments

2012 ◽  
Vol 7 (1) ◽  
Author(s):  
Federico Fogolari ◽  
Alessandra Corazza ◽  
Paolo Viglino ◽  
Gennaro Esposito
Keyword(s):  
Protein Fragments ◽  
Structure Similarity ◽  
Protein Models ◽  
Similarity Searches

scholarly journals Pairwise running of automated crystallographic model-building pipelines

2020 ◽  
Vol 76 (9) ◽  
pp. 814-823 ◽  
Author(s):  
Emad Alharbi ◽  
Radu Calinescu ◽  
Kevin Cowtan
Keyword(s):  
Model Building ◽  
Protein Structures ◽  
Data Sets ◽  
Protein Model

For the last two decades, researchers have worked independently to automate protein model building, and four widely used software pipelines have been developed for this purpose: ARP/wARP, Buccaneer, Phenix AutoBuild and SHELXE. Here, the usefulness of combining these pipelines to improve the built protein structures by running them in pairwise combinations is examined. The results show that integrating these pipelines can lead to significant improvements in structure completeness and R free. In particular, running Phenix AutoBuild after Buccaneer improved structure completeness for 29% and 75% of the data sets that were examined at the original resolution and at a simulated lower resolution, respectively, compared with running Phenix AutoBuild on its own. In contrast, Phenix AutoBuild alone produced better structure completeness than the two pipelines combined for only 7% and 3% of these data sets.

scholarly journals Estimating local protein model quality: prospects for molecular replacement

2020 ◽  
Vol 76 (3) ◽  
pp. 285-290
Author(s):  
Björn Wallner
Keyword(s):  
Error Estimates ◽  
Added Value ◽  
Local Error ◽  
Molecular Replacement ◽  
Model Quality ◽  
Data Set ◽  
Protein Model ◽  
Protein Models ◽  
Local Protein

Model quality assessment programs estimate the quality of protein models and can be used to estimate local error in protein models. ProQ3D is the most recent and most accurate version of our software. Here, it is demonstrated that it is possible to use local error estimates to substantially increase the quality of the models for molecular replacement (MR). Adjusting the B factors using ProQ3D improved the log-likelihood gain (LLG) score by over 50% on average, resulting in significantly more successful models in MR compared with not using error estimates. On a data set of 431 homology models to address difficult MR targets, models with error estimates from ProQ3D received an LLG of >50 for almost half of the models 209/431 (48.5%), compared with 175/431 (40.6%) for the previous version, ProQ2, and only 74/431 (17.2%) for models with no error estimates, clearly demonstrating the added value of using error estimates to enable MR for more targets. ProQ3D is available from http://proq3.bioinfo.se/ both as a server and as a standalone download.

scholarly journals 223 Lesch-Nyhan syndrome: from patient to mouse model

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 46-47
Author(s):  
Marina V Kubekina ◽  
Vladislav A Kalmykov ◽  
Pavel A Kusov ◽  
Yulya Y Silaeva ◽  
Alexei V Deikin
Keyword(s):  
Mouse Model ◽  
Structural Changes ◽  
Structural Model ◽  
Gene Mutations ◽  
Russian Science ◽  
Transgenic Organisms ◽  
Protein Model ◽  
Hypoxanthine Guanine Phosphoribosyltransferase ◽  
Academy Of Sciences ◽  
Protein Models

Abstract Introduction. HPRT1 is a Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) coding gene, mutations of which cause, among other diseases, Lesch-Nyhan syndrome. LNS is a severe X-linked recessive neurological disorder. Alignment shows 98.6% homology of human and murine protein sequences. Objectives. We assume that murine model of this human disease should be developed. So, our purpose is to create a transgenic mouse model of Lesch-Nyhan syndrome by CRISPR/Cas9 genome editing system. Methods. The BLAST was used to find homologous mutation in murine HPRT1 gene comparing to Human one. X-ray crystallographic structural model of the HPRT1 was used as template for M4T Raptor algorithm to generate predicted structure of mutated protein. Models were visualized in PyMol (Schrodinger, Portland, OR). Lack of enzymatic activity of the HGPRT could be caused via troubled homodimerization. Absence of the aliphatic Valine could be the reason of the hindered monomers interaction. Genetic construction based on the px330 plasmid was brought using microinjection method in mouse fertilized ovum for producing primary transgenic organisms. Results. The CRISPR/Cas9 system was specifically designed to carry out mutations in HPRT. The resulting genetic construct was introduced into the fertilized mouse ovum to obtain primary transgenic organisms. This mouse was obtained at the Institute of Biology of the Russian Academy of Sciences. Conclusion. Homologous mutation in human and murine HPRT1 gene resulting into comparable conformational change in the protein model structure was revealed, so murine personalized model of the Lesch-Nyhan syndrome could be developed. Structural changes can be further studied to provide treatment strategy for people suffering from Lesch-Nyhan syndrome. This study was supported by Russian Science Foundation (Grant #17-75-20249).

scholarly journals SELECTIVE ADVANTAGE OF RECOMBINATION IN EVOLVING PROTEIN POPULATIONS: A LATTICE MODEL STUDY

2006 ◽  
Vol 17 (01) ◽  
pp. 75-90 ◽  
Author(s):  
PAUL D. WILLIAMS ◽  
DAVID D. POLLOCK ◽  
RICHARD A. GOLDSTEIN
Keyword(s):  
Homologous Recombination ◽  
Lattice Model ◽  
Selective Advantage ◽  
Native Structure ◽  
Fitness Level ◽  
Model Study ◽  
Protein Model ◽  
Evolutionary Advantage ◽  
Protein Models ◽  
Mutational Processes

Recent research has attempted to clarify the contributions of several mutational processes, such as substitutions or homologous recombination. Simplistic, tractable protein models, which determine the compact native structure phenotype from the sequence genotype, are well-suited to such studies. In this paper, we use a lattice-protein model to examine the effects of point mutation and homologous recombination on evolving populations of proteins. We find that while the majority of mutation and recombination events are neutral or deleterious, recombination is far more likely to be beneficial. This results in a faster increase in fitness during evolution, although the final fitness level is not significantly changed. This transient advantage provides an evolutionary advantage to subpopulations that undergo recombination, allowing fixation of recombination to occur in the population.

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