Computational Tools for Structural Analysis with Uncertainties: Software Technology and Large-Scale Applications

2009 ◽  
pp. 25-54
Author(s):  
G.I. Schuëller ◽  
M.F. Pellissetti
Keyword(s):  
Structural Analysis ◽  
Large Scale ◽  
Computational Tools ◽  
Software Technology

scholarly journals Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches

2021 ◽  
Author(s):  
Mehdi A. Beniddir ◽  
Kyo Bin Kang ◽  
Grégory Genta-Jouve ◽  
Florian Huber ◽  
Simon Rogers ◽  
...  
Keyword(s):  
Natural Product ◽  
Large Scale ◽  
Scale Analysis ◽  
Computational Tools ◽  
Natural Product Discovery ◽  
Large Scale Analysis ◽  
Metabolite Annotation

This review highlights the key computational tools and emerging strategies for metabolite annotation, and discusses how these advances will enable integrated large-scale analysis to accelerate natural product discovery.

scholarly journals The daunting polygenicity of mental illness: making a new map

2018 ◽  
Vol 373 (1742) ◽  
pp. 20170031 ◽  
Author(s):  
Steven E. Hyman
Keyword(s):  
Mental Health ◽  
Large Scale ◽  
Computational Models ◽  
Model Organisms ◽  
Human Biology ◽  
Genetic Studies ◽  
Computational Tools ◽  
Experimental Systems ◽  
Terra Incognita ◽  
Phenotypic Complexity

An epochal opportunity to elucidate the pathogenic mechanisms of psychiatric disorders has emerged from advances in genomic technology, new computational tools and the growth of international consortia committed to data sharing. The resulting large-scale, unbiased genetic studies have begun to yield new biological insights and with them the hope that a half century of stasis in psychiatric therapeutics will come to an end. Yet a sobering picture is coming into view; it reveals daunting genetic and phenotypic complexity portending enormous challenges for neurobiology. Successful exploitation of results from genetics will require eschewal of long-successful reductionist approaches to investigation of gene function, a commitment to supplanting much research now conducted in model organisms with human biology, and development of new experimental systems and computational models to analyse polygenic causal influences. In short, psychiatric neuroscience must develop a new scientific map to guide investigation through a polygenic terra incognita . This article is part of a discussion meeting issue ‘Of mice and mental health: facilitating dialogue between basic and clinical neuroscientists’.

scholarly journals TADOSS: computational estimation of tandem domain swap stability

2018 ◽  
Vol 35 (14) ◽  
pp. 2507-2508 ◽  
Author(s):  
Aleix Lafita ◽  
Pengfei Tian ◽  
Robert B Best ◽  
Alex Bateman
Keyword(s):  
Large Scale ◽  
Domain Swapping ◽  
Coarse Grained ◽  
Supplementary Information ◽  
Simulation Studies ◽  
Computational Tools ◽  
Domain Swap ◽  
Computational Estimation ◽  
High Propensity ◽  
The Stability

Abstract Summary Proteins with highly similar tandem domains have shown an increased propensity for misfolding and aggregation. Several molecular explanations have been put forward, such as swapping of adjacent domains, but there is a lack of computational tools to systematically analyze them. We present the TAndem DOmain Swap Stability predictor (TADOSS), a method to computationally estimate the stability of tandem domain-swapped conformations from the structures of single domains, based on previous coarse-grained simulation studies. The tool is able to discriminate domains susceptible to domain swapping and to identify structural regions with high propensity to form hinge loops. TADOSS is a scalable method and suitable for large scale analyses. Availability and implementation Source code and documentation are freely available under an MIT license on GitHub at https://github.com/lafita/tadoss. Supplementary information Supplementary data are available at Bioinformatics online.

Adaptive-Curvature Structures with Auxetic Materials

2018 ◽  
Vol 1149 ◽  
pp. 53-63
Author(s):  
Roberto Naboni ◽  
Stefano Sartori ◽  
Lorenzo Mirante
Keyword(s):  
Large Scale ◽  
Morphological Features ◽  
Geometrical Parameters ◽  
Computational Tools ◽  
Auxetic Materials ◽  
Initial Geometry ◽  
Tools And Methods

Advancements in computational tools are offering designers the possibility to change their relationship with materials and establishing new synergies between matter, form and behaviour. This work explores this paradigm by introducing the use of auxetic metamaterials, specifically engineered to obtain properties beyond those found in nature, to generate structures with adaptive curvature obtained from planar construction elements. It is discussed how through programming an initial geometry with the strategic negotiation of several geometrical parameters it is possible to control finely the structural and morphological features of a structure. The paper presents approach, tools and methods for designing auxetics for large scale applications, and use them to create heterogeneous active-bending structures.

scholarly journals Independent and complementary methods for large-scale structural analysis of mammalian chromatin

2007 ◽  
Vol 17 (6) ◽  
pp. 928-939 ◽  
Author(s):  
J. H. Dennis ◽  
H.-Y. Fan ◽  
S. M. Reynolds ◽  
G. Yuan ◽  
J. C. Meldrim ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Large Scale ◽  
Complementary Methods
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