scholarly journals Improved low-resolution crystallographic refinement with Phenix and Rosetta

2014 ◽  
Vol 70 (a1) ◽  
pp. C782-C782
Author(s):  
Nathaniel Echols ◽  
Frank DiMaio ◽  
Jeffrey Headd ◽  
Thomas Terwilliger ◽  
David Baker ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Model Building ◽  
New Method ◽  
Low Resolution ◽  
Final Model ◽  
Software Packages ◽  
Advanced Sampling ◽  
Model Geometry ◽  
Improved Model ◽  
R Factors

Refinement of macromolecular structures against low-resolution crystallographic data is limited by the ability of current methods to arrive at a high-quality structure with realistic geometry. We have developed a new method for crystallographic refinement which combines the Rosetta sampling methodology and all atom energy function with likelihood-based reciprocal space refinement in Phenix, and find, on a test set of difficult low-resolution refinement cases, that models refined with the new method have significantly improved model geometry, and in most cases, lower free R factors and RMS deviation to the final model. Integration of the software packages additionally makes advanced sampling methods used in structure prediction and design available for crystallographic refinement and model-building, and also provides a strategy for improving the Rosetta force field for better agreement with experimental data.

scholarly journals A mosaic bulk-solvent model improves density maps and the fit between model and data

2021 ◽  
Author(s):  
Pavel V. Afonine ◽  
Paul D. Adams ◽  
Oleg V Sobolev ◽  
Alexandre Urzhumtsev
Keyword(s):  
Protein Data Bank ◽  
Model Building ◽  
Data Bank ◽  
Crystallographic Data ◽  
Software Packages ◽  
Map Interpretation ◽  
Density Maps ◽  
Solvent Model ◽  
Modeling Power ◽  
R Factors

Bulk solvent is a major component of bio-macromolecular crystals and therefore contributes significantly to diffraction intensities. Accurate modeling of the bulk-solvent region has been recognized as important for many crystallographic calculations, from computing of R-factors and density maps to model building and refinement. Owing to its simplicity and computational and modeling power, the flat (mask-based) bulk-solvent model introduced by Jiang & Brunger (1994) is used by most modern crystallographic software packages to account for disordered solvent. In this manuscript we describe further developments of the mask-based model that improves the fit between the model and the data and aids in map interpretation. The new algorithm, here referred to as mosaic bulk-solvent model, considers solvent variation across the unit cell. The mosaic model is implemented in the computational crystallography toolbox and can be used in Phenix in most contexts where accounting for bulk-solvent is required. It has been optimized and validated using a sufficiently large subset of the Protein Data Bank entries that have crystallographic data available.

scholarly journals ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

2018 ◽  
Vol 74 (6) ◽  
pp. 519-530 ◽  
Author(s):  
Tristan Ian Croll
Keyword(s):  
Electron Density ◽  
Model Building ◽  
Low Resolution ◽  
Minichromosome Maintenance ◽  
Molecular Graphics ◽  
Final Model ◽  
Density Maps ◽  
Resolution Electron ◽  
Resolution Model

This paper introducesISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps.ISOLDEcombines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated howISOLDEcan be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.

scholarly journals FOLDING ELASTIC TRANSMEMBRANE HELICES TO FIT IN A LOW-RESOLUTION IMAGE BY ELECTRON MICROSCOPY

2011 ◽  
Vol 09 (supp01) ◽  
pp. 37-50 ◽  
Author(s):  
YUTAKA UENO ◽  
KAZUNORI KAWASAKI ◽  
OSAMU SAITO ◽  
MASAFUMI ARAI ◽  
MAKIKO SUWA
Keyword(s):  
Membrane Proteins ◽  
Structure Prediction ◽  
Molecular Model ◽  
Imaging Techniques ◽  
Transmembrane Helix ◽  
Prediction Method ◽  
Molecular Shape ◽  
Coarse Grained ◽  
Transmembrane Helices ◽  
Low Resolution

Structure prediction of membrane proteins could be constrained and thereby improved by introducing data of the observed molecular shape. We studied a coarse-grained molecular model that relied on residue-based dummy atoms to fold the transmembrane helices of a protein in the observed molecular shape. Based on the inter-residue potential, the α-helices were folded to contact each other in a simulated annealing protocol to search optimized conformation. Fitting the model into a three-dimensional volume was tested for proteins with known structures and resulted in a fairly reasonable arrangement of helices. In addition, the constraint to the packing transmembrane helix with the two-dimensional region was tested and found to work as a very similar folding guide. The obtained models nicely represented α-helices with the desired slight bend. Our structure prediction method for membrane proteins well demonstrated reasonable folding results using a low-resolution structural constraint introduced from recent cell-surface imaging techniques.

scholarly journals Incremental model breakdown to assess the multi-hypotheses problem

2018 ◽  
Vol 22 (8) ◽  
pp. 4565-4581 ◽  
Author(s):  
Florian U. Jehn ◽  
Lutz Breuer ◽  
Tobias Houska ◽  
Konrad Bestian ◽  
Philipp Kraft
Keyword(s):  
Hydrological Modeling ◽  
Model Performance ◽  
Complex Model ◽  
Model Parameters ◽  
Objective Functions ◽  
Final Model ◽  
Incremental Model ◽  
Model Efficiency ◽  
Improved Model ◽  
Model Structures

Abstract. The ambiguous representation of hydrological processes has led to the formulation of the multiple hypotheses approach in hydrological modeling, which requires new ways of model construction. However, most recent studies focus only on the comparison of predefined model structures or building a model step by step. This study tackles the problem the other way around: we start with one complex model structure, which includes all processes deemed to be important for the catchment. Next, we create 13 additional simplified models, where some of the processes from the starting structure are disabled. The performance of those models is evaluated using three objective functions (logarithmic Nash–Sutcliffe; percentage bias, PBIAS; and the ratio between the root mean square error and the standard deviation of the measured data). Through this incremental breakdown, we identify the most important processes and detect the restraining ones. This procedure allows constructing a more streamlined, subsequent 15th model with improved model performance, less uncertainty and higher model efficiency. We benchmark the original Model 1 and the final Model 15 with HBV Light. The final model is not able to outperform HBV Light, but we find that the incremental model breakdown leads to a structure with good model performance, fewer but more relevant processes and fewer model parameters.

scholarly journals MODELING OF THE JACKED PILE STATIC LOAD TEST WITH PLAXIS 3D / SPAUSTINIO POLIO BANDYMO STATINE APKROVA MODELIAVIMAS PLAXIS 3D

2016 ◽  
Vol 8 (5) ◽  
pp. 495-498
Author(s):  
Tautvydas Statkus
Keyword(s):  
Building Materials ◽  
Model Building ◽  
Static Load ◽  
Load Test ◽  
Static Load Test ◽  
Model Geometry ◽  
Comparison Of The Results ◽  
3D Software ◽  
Installation Technology ◽  
Plaxis 3D

In this article jacked pile installation technology and its current processes, altering the base physical and mechanical characteristics are discussed. For the jacked pile static load test simulation Plax 3D software was selected, the opportunities and developments were described. Model building, materials, models, model geometry, finite elements, boundary conditions and assumptions adopted in addressing problems described in detail. Three different tasks formulated and load-settlement dependence a comparison of the results with the experiment given. Conclusions are formulated according to the modeling results. Šiame straipsnyje aptarta spaustinių polių įrengimo technologija ir ją taikant vykstantys procesai, keičiantys pagrindo fizines ir mechanines charakteristikas. Spaustinio polio bandymui statine apkrova modeliuoti pasirinktas PLAXIS 3D programinis paketas ir aprašytos jo galimybės bei raida. Detaliai nupasakotas modelio kūrimas, medžiagų modeliai, modelio geometrija, baigtiniai elementai, kraštinės sąlygos ir priimamos prielaidos sprendžiant problemą. Suformuluoti trys sprendžiami uždaviniai ir apkrovos bei nuosėdžio priklausomybe pateikiamas rezultatų palyginimas su eksperimentu. Atsižvelgiant į modeliavimo rezultatus suformuluotos išvados.

Predicting RNA Secondary Structure Using a Improved BPSO Based on Stem Combination

2013 ◽  
Vol 325-326 ◽  
pp. 1551-1554
Author(s):  
Yi Qi
Keyword(s):  
Secondary Structure ◽  
Sensitivity And Specificity ◽  
Rna Structure ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Experimental Results ◽  
New Method ◽  
Rna Structure Prediction ◽  
New Strategies

In this paper, we present an improved BPSO to predict RNA secondary structure to improve the performance with two new strategies. First one is to reduce the searching space of PSO through super stem set construction. Second is to modify the general BPSO updating process to settle stem permutation and combination problems. The experimental results show that the new method is effective for RNA structure prediction in terms of sensitivity and specificity by different sequence datasets including simple pseudoknot.

On the Use of low-resolution Data to Improve Structure Prediction of Proteins and Protein Complexes

2009 ◽  
Vol 5 (11) ◽  
pp. 3129-3137 ◽  
Author(s):  
Marco D’Abramo ◽  
Tim Meyer ◽  
Pau Bernadó ◽  
Carles Pons ◽  
Juan Fernández Recio ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Protein Complexes ◽  
Low Resolution ◽  
Resolution Data

scholarly journals Rapid model building of α-helices in electron-density maps

2010 ◽  
Vol 66 (3) ◽  
pp. 268-275 ◽  
Author(s):  
Thomas C. Terwilliger
Keyword(s):  
High Resolution ◽  
Electron Density ◽  
Model Building ◽  
Main Chain ◽  
Rapid Identification ◽  
Side Chains ◽  
Low Resolution ◽  
Density Maps ◽  
Experimental Electron Density

A method for the identification of α-helices in electron-density maps at low resolution followed by interpretation at moderate to high resolution is presented. Rapid identification is achieved at low resolution, where α-helices appear as tubes of density. The positioning and direction of the α-helices is obtained at moderate to high resolution, where the positions of side chains can be seen. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 Å. An average of 63% of the α-helical residues in these proteins were built and an average of 76% of the residues built matched helical residues in the refined models of the proteins. The overall average r.m.s.d. between main-chain atoms in the modeled α-helices and the nearest atom with the same name in the refined models of the proteins was 1.3 Å.

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