scholarly journals Novel sampling strategies and a coarse‐grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37–45

2019 ◽  
Vol 88 (8) ◽  
pp. 973-985 ◽  
Author(s):  
Shourya S. Roy Burman ◽  
Morgan L. Nance ◽  
Jeliazko R. Jeliazkov ◽  
Jason W. Labonte ◽  
Joseph H. Lubin ◽  
...  
Keyword(s):  
Score Function ◽  
Coarse Grained ◽  
Sampling Strategies

scholarly journals Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI Rounds 37–45

2019 ◽  
Author(s):  
Shourya S. Roy Burman ◽  
Morgan L. Nance ◽  
Jeliazko R. Jeliazkov ◽  
Jason W. Labonte ◽  
Joseph H. Lubin ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Score Function ◽  
Coarse Grained ◽  
Sampling Strategies ◽  
Scoring Methods ◽  
Flexible Docking ◽  
Multi Stage ◽  
Docking Protocol ◽  
Protein Backbones

AbstractCAPRI Rounds 37 through 45 introduced larger complexes, new macromolecules, and multi-stage assemblies. For these rounds, we used and expanded docking methods in Rosetta to model 23 target complexes. We successfully predicted 14 target complexes and recognized and refined near-native models generated by other groups for two further targets. Notably, for targets T110 and T136, we achieved the closest prediction of any CAPRI participant. We created several innovative approaches during these rounds. Since Round 39 (target 122), we have used the new RosettaDock 4.0, which has a revamped coarse-grained energy function and the ability to perform conformer selection during docking with hundreds of pre-generated protein backbones. Ten of the complexes had some degree of symmetry in their interactions, so we tested Rosetta SymDock, realized its shortcomings, and developed the next-generation symmetric docking protocol, SymDock2, which includes docking of multiple backbones and induced-fit refinement. Since the last CAPRI assessment, we also developed methods for modeling and designing carbohydrates in Rosetta, and we used them to successfully model oligosaccharide–protein complexes in Round 41. While the results were broadly encouraging, they also highlighted the pressing need to invest in (1) flexible docking algorithms with the ability to model loop and linker motions and in (2) new sampling and scoring methods for oligosaccharide–protein interactions.

scholarly journals Flexible backbone assembly and refinement of symmetrical homomeric complexes

2018 ◽  
Author(s):  
Shourya S. Roy Burman ◽  
Remy A. Yovanno ◽  
Jeffrey J. Gray
Keyword(s):  
Protein Structures ◽  
Score Function ◽  
Conformational Space ◽  
Coarse Grained ◽  
List Type ◽  
Promising Alternative ◽  
Computational Docking ◽  
Realistic Modeling ◽  
High Resolution Structure ◽  
Resolution Structure

SummarySymmetrical homomeric proteins are ubiquitous in every domain of life, and information about their structure is essential to decipher function. The size of these complexes often makes them intractable to high-resolution structure determination experiments. Computational docking algorithms offer a promising alternative for modeling large complexes with arbitrary symmetry. Accuracy of existing algorithms, however, is limited by backbone inaccuracies when using homology-modeled monomers. Here, we present Rosetta SymDock2 with a broad search of symmetrical conformational space using a six-dimensional coarse-grained score function followed by an all-atom flexible-backbone refinement, which we demonstrate to be essential for physically-realistic modeling of tightly packed complexes. In global docking of a benchmark set of complexes of different point symmetries — staring from homology-modeled monomers — we successfully dock (defined as predicting three near-native structures in the five top-scoring models) 19 out of 31 cyclic complexes and 5 out of 12 dihedral complexes.HighlightsSymDock2 is an algorithm to assemble symmetric protein structures from monomersCoarse-grained score function discriminates near-native conformationsFlexible backbone refinement is necessary to create realistic all-atom modelsResults improve six-fold and outperform other symmetric docking algorithmsGraphical Abstract

The Alteration of the Pore Spaces in Sandstones

1973 ◽  
Vol 31 ◽  
pp. 210-211
Author(s):  
R. E. Ferrell ◽  
G. G. Paulson
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
The Other ◽  
Coarse Grained ◽  
Depositional Fabric ◽  
Soluble Components ◽  
Scanning Electron ◽  
Shape And Size

The pore spaces in sandstones are the result of the original depositional fabric and the degree of post-depositional alteration that the rock has experienced. The largest pore volumes are present in coarse-grained, well-sorted materials with high sphericity. The chief mechanisms which alter the shape and size of the pores are precipitation of cementing agents and the dissolution of soluble components. Each process may operate alone or in combination with the other, or there may be several generations of cementation and solution.The scanning electron microscope has ‘been used in this study to reveal the morphology of the pore spaces in a variety of moderate porosity, orthoquartzites.

On the Origin of the Microscystalline Structure in Rapidly Solidified IN-100 Powder

1977 ◽  
Vol 35 ◽  
pp. 260-261
Author(s):  
J. M. Walsh ◽  
K. P. Gumz ◽  
J. C. Whittles ◽  
B. H. Kear
Keyword(s):  
The Other ◽  
Coarse Grained ◽  
Microcrystalline Structure ◽  
Routine Examination ◽  
Atomization Process ◽  
Centrifugal Atomization ◽  
Splat Quenching ◽  
Powder Particles ◽  
Dendritic Microstructures ◽  
Rapidly Solidified

During a routine examination of the microstructure of rapidly solidified IN-100 powder, produced by a newly-developed centrifugal atomization process1, essentially two distinct types of microstructure were identified. When a high melt superheat is maintained during atomization, the powder particles are predominantly coarse-grained, equiaxed or columnar, with distinctly dendritic microstructures, Figs, la and 4a. On the other hand, when the melt superheat is reduced by increasing the heat flow to the disc of the rotary atomizer, the powder particles are predominantly microcrystalline in character, with typically one dendrite per grain, Figs, lb and 4b. In what follows, evidence is presented that strongly supports the view that the unusual microcrystalline structure has its origin in dendrite erosion occurring in a 'mushy zone' of dynamic solidification on the disc of the rotary atomizer.The critical observations were made on atomized material that had undergone 'splat-quenching' on previously solidified, chilled substrate particles.

Correlation between dislocation, grain boundary and interface of duplex SS in stress corrosion cracking(SCC)

1990 ◽  
Vol 48 (4) ◽  
pp. 928-929
Author(s):  
Wang Zheng-fang ◽  
Z.F. Wang
Keyword(s):  
Stainless Steel ◽  
Thermal Cycle ◽  
Secondary Phase ◽  
Corrosion Cracking ◽  
Coarse Grained ◽  
Test Environment ◽  
Fine Grained ◽  
Evaluation Test ◽  
Welding Thermal Cycle ◽  
Micro Analysis

The main purpose of this study highlights on the evaluation of chloride SCC resistance of the material,duplex stainless steel,OOCr18Ni5Mo3Si2 (18-5Mo) and its welded coarse grained zone(CGZ).18-5Mo is a dual phases (A+F) stainless steel with yield strength:512N/mm2 .The proportion of secondary Phase(A phase) accounts for 30-35% of the total with fine grained and homogeneously distributed A and F phases(Fig.1).After being welded by a specific welding thermal cycle to the material,i.e. Tmax=1350°C and t8/5=20s,microstructure may change from fine grained morphology to coarse grained morphology and from homogeneously distributed of A phase to a concentration of A phase(Fig.2).Meanwhile,the proportion of A phase reduced from 35% to 5-10°o.For this reason it is known as welded coarse grained zone(CGZ).In association with difference of microstructure between base metal and welded CGZ,so chloride SCC resistance also differ from each other.Test procedures:Constant load tensile test(CLTT) were performed for recording Esce-t curve by which corrosion cracking growth can be described, tf,fractured time,can also be recorded by the test which is taken as a electrochemical behavior and mechanical property for SCC resistance evaluation. Test environment:143°C boiling 42%MgCl2 solution is used.Besides, micro analysis were conducted with light microscopy(LM),SEM,TEM,and Auger energy spectrum(AES) so as to reveal the correlation between the data generated by the CLTT results and micro analysis.

Who owns a personal home page?

2003 ◽  
Vol 62 (2) ◽  
pp. 121-129 ◽  
Author(s):  
Astrid Schütz ◽  
Franz Machilek
Keyword(s):  
Search Engine ◽  
Home Page ◽  
Sampling Strategies ◽  
Home Pages ◽  
Personal Home Pages ◽  
Age And Sex

Research on personal home pages is still rare. Many studies to date are exploratory, and the problem of drawing a sample that reflects the variety of existing home pages has not yet been solved. The present paper discusses sampling strategies and suggests a strategy based on the results retrieved by a search engine. This approach is used to draw a sample of 229 personal home pages that portray private identities. Findings on age and sex of the owners and elements characterizing the sites are reported.

Input of coarse-grained siliciclastics into the Pyrenean Basin during the PETM (1): overview

2014 ◽  
Vol 31 ◽  
pp. 177-178
Author(s):  
Victoriano Pujalte ◽  
Juan Ignacio Baceta ◽  
Birger Schmitz
Keyword(s):  
Coarse Grained

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

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