Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bendix: intuitive helix geometry analysis and abstraction.

ABSTRACT:

Unlabelled

The flexibility of α-helices is important for membrane protein function and calls for better visualization and analysis. Software is presented that quantifies and projects the helix axis evolution over time, with the choice of uniform or analytic heatmap graphics according to the local geometry. Bendix supports static, molecular dynamics, atomistic and coarse-grained input.

Availability and implementation

Bendix source code and documentation, including installation instructions, are freely available at http://sbcb.bioch.ox.ac.uk/Bendix. Bendix is written in Tcl as an extension to VMD and is supported by all major operating systems.

SUBMITTER: Dahl AC

PROVIDER: S-EPMC3413393 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Bendix: intuitive helix geometry analysis and abstraction.

Dahl Anna Caroline E AC Chavent Matthieu M Sansom Mark S P MS

Bioinformatics (Oxford, England) 20120623 16

<h4>Unlabelled</h4>The flexibility of α-helices is important for membrane protein function and calls for better visualization and analysis. Software is presented that quantifies and projects the helix axis evolution over time, with the choice of uniform or analytic heatmap graphics according to the local geometry. Bendix supports static, molecular dynamics, atomistic and coarse-grained input.<h4>Availability and implementation</h4>Bendix source code and documentation, including installation inst ...[more]

PMID: 22730430

Similar Datasets

Object geometry serves humans' intuitive physics of stability.

Project description:How do humans judge physical stability? A prevalent account emphasizes the mental simulation of physical events implemented by an intuitive physics engine in the mind. Here we test the extent to which the perceptual features of object geometry are sufficient for supporting judgments of falling direction. In all experiments, adults and children judged the falling direction of a tilted object and, across experiments, objects differed in the geometric features (i.e., geometric centroid, object height, base size and/or aspect ratio) relevant to the judgment. Participants' performance was compared to computational models trained on geometric features, as well as a deep convolutional neural network (ResNet-50), none of which incorporated mental simulation. Adult and child participants' performance was well fit by models of object geometry, particularly the geometric centroid. ResNet-50 also provided a good account of human performance. Altogether, our findings suggest that object geometry may be sufficient for judging the falling direction of tilted objects, independent of mental simulation.

| S-EPMC10799025 | biostudies-literature

An Algorithm for Protein Helix Assignment Using Helix Geometry.

Project description:Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment. In this paper we present a two-step assignment algorithm. The first step searches for a series of bona fide helical curves each one best fits the coordinates of four successive backbone Cα atoms. The second step uses the best fit helical curves as input to make helix assignment. The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 310 and π helices as well as their left-handed versions. One salient feature of the algorithm is that the assigned helices are structurally more uniform than those by the previous programs. The structural uniformity should be useful for protein structure classification and prediction while the accurate assignment of a helix to a particular type underlies structure-function relationship in proteins.

| S-EPMC4488512 | biostudies-literature

The Geometry of Abstraction in the Hippocampus and Prefrontal Cortex.

Project description:The curse of dimensionality plagues models of reinforcement learning and decision making. The process of abstraction solves this by constructing variables describing features shared by different instances, reducing dimensionality and enabling generalization in novel situations. Here, we characterized neural representations in monkeys performing a task described by different hidden and explicit variables. Abstraction was defined operationally using the generalization performance of neural decoders across task conditions not used for training, which requires a particular geometry of neural representations. Neural ensembles in prefrontal cortex, hippocampus, and simulated neural networks simultaneously represented multiple variables in a geometry reflecting abstraction but that still allowed a linear classifier to decode a large number of other variables (high shattering dimensionality). Furthermore, this geometry changed in relation to task events and performance. These findings elucidate how the brain and artificial systems represent variables in an abstract format while preserving the advantages conferred by high shattering dimensionality.

| S-EPMC8451959 | biostudies-literature

The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions.

Project description:α Helices are a basic unit of protein secondary structure and therefore the interaction between helices is crucial to understanding tertiary and higher-order folds. Comparing subtle variations in the structural and sequence motifs between membrane and soluble proteins sheds light on the different constraints faced by each environment and elucidates the complex puzzle of membrane protein folding. Here, we demonstrate that membrane and water-soluble helix pairs share a small number of similar folds with various interhelical distances. The composition of the residues that pack at the interface between corresponding motifs shows that hydrophobic residues tend to be more enriched in the water-soluble class of structures and small residues in the transmembrane class. The latter group facilitates packing via sidechain- and backbone-mediated hydrogen bonds within the low-dielectric membrane milieu. The helix-helix interactome space, with its associated sequence preferences and accompanying hydrogen-bonding patterns, should be useful for engineering, prediction, and design of protein structure.

| S-EPMC4351763 | biostudies-literature

A thermophilic phage uses a small terminase protein with a fixed helix-turn-helix geometry.

Project description:Tailed bacteriophages use a DNA-packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component of this DNA-packaging machinery acts as a molecular matchmaker that recognizes both the viral genome and the main motor component, the large terminase (TerL). However, how TerS binds DNA and the TerL protein remains unclear. Here we identified gp83 of the thermophilic bacteriophage P74-26 as the TerS protein. We found that TerSP76-26 oligomerizes into a nonamer that binds DNA, stimulates TerL ATPase activity, and inhibits TerL nuclease activity. A cryo-EM structure of TerSP76-26 revealed that it forms a ring with a wide central pore and radially arrayed helix-turn-helix domains. The structure further showed that these helix-turn-helix domains, which are thought to bind DNA by wrapping the double helix around the ring, are rigidly held in an orientation distinct from that seen in other TerS proteins. This rigid arrangement of the putative DNA-binding domain imposed strong constraints on how TerSP76-26 can bind DNA. Finally, the TerSP76-26 structure lacked the conserved C-terminal β-barrel domain used by other TerS proteins for binding TerL. This suggests that a well-ordered C-terminal β-barrel domain is not required for TerSP76-26 to carry out its matchmaking function. Our work highlights a thermophilic system for studying the role of small terminase proteins in viral maturation and presents the structure of TerSP76-26, revealing key differences between this thermophilic phage and its mesophilic counterparts.

| S-EPMC7086035 | biostudies-literature

Predicting the helix packing of globular proteins by self-correcting distance geometry.

Project description:A new self-correcting distance geometry method for predicting the three-dimensional structure of small globular proteins was assessed with a test set of 8 helical proteins. With the knowledge of the amino acid sequence and the helical segments, our completely automated method calculated the correct backbone topology of six proteins. The accuracy of the predicted structures ranged from 2.3 A to 3.1 A for the helical segments compared to the experimentally determined structures. For two proteins, the predicted constraints were not restrictive enough to yield a conclusive prediction. The method can be applied to all small globular proteins, provided the secondary structure is known from NMR analysis or can be predicted with high reliability.

| S-EPMC2143125 | biostudies-other

The ribosome prohibits the G•U wobble geometry at the first position of the codon-anticodon helix.

Project description:Precise conversion of genetic information into proteins is essential to cellular health. However, a margin of error exists and is at its highest on the stage of translation of mRNA by the ribosome. Here we present three crystal structures of 70S ribosome complexes with messenger RNA and transfer RNAs and show that when a G•U base pair is at the first position of the codon-anticodon helix a conventional wobble pair cannot form because of inescapable steric clash between the guanosine of the A codon and the key nucleotide of decoding center adenosine 1493 of 16S rRNA. In our structure the rigid ribosomal decoding center, which is identically shaped for cognate or near-cognate tRNAs, forces this pair to adopt a geometry close to that of a canonical G•C pair. We further strengthen our hypothesis that spatial mimicry due either to base tautomerism or ionization dominates the translation infidelity mechanism.

| S-EPMC5291260 | biostudies-literature

Mindful and Intuitive Eating Imagery on Instagram: A Content Analysis.

Project description:Non-dieting approaches, including mindful/intuitive eating, to health improvement are of increasing interest, yet little is known about young adults' social media exposure to them. Therefore, this study aimed to describe the imagery related to mindful/intuitive eating which is visible to young adult Instagram users. Images categorized under the hashtags 'mindfuleating' and 'intuitiveeating' were searched in September 2021 using the 'top posts' view. Screen captures of 1200 grid-view images per hashtag were used to construct coding frameworks and to determine saturation. Sample sizes for #mindfuleating and #intuitiveeating were 405 and 495 images, respectively. Individual images were coded collaboratively. Almost half of each sample depicted food or drink, of which 50-60% were healthy foods. Approximately 17% were single-person images, of which the majority were young, female adults with healthy weight. Approximately one-third of text suggested credibility through credentials, profession, or evidence. Messaging was similar for both hashtags, encompassing mindful/intuitive eating (~40%), nutrition/eating behaviours (~15%), physical/mental health (~20%), disordered eating (~12%), and body-/self-acceptance (~12%). Differences were observed between hashtags for weight-related concepts (20%/1%) and anti-diet/weight-neutral approaches (10%/35%). The representation on Instagram of mindful and intuitive eating portrays healthy lifestyles without a focus on weight but lacks demographical and body-type diversity. Instagram holds the potential for health professionals to disseminate culturally/demographically inclusive, evidence-based health/nutrition information to youth.

| S-EPMC9502653 | biostudies-literature

Phylogenetic analysis of the human basic helix-loop-helix proteins.

Project description:BackgroundThe basic helix-loop-helix (bHLH) proteins are a large and complex multigene family of transcription factors with important roles in animal development, including that of fruitflies, nematodes and vertebrates. The identification of orthologous relationships among the bHLH genes from these widely divergent taxa allows reconstruction of the putative complement of bHLH genes present in the genome of their last common ancestor.ResultsWe identified 39 different bHLH genes in the worm Caenorhabditis elegans, 58 in the fly Drosophila melanogaster and 125 in human (Homo sapiens). We defined 44 orthologous families that include most of these bHLH genes. Of these, 43 include both human and fly and/or worm genes, indicating that genes from these families were already present in the last common ancestor of worm, fly and human. Only two families contain both yeast and animal genes, and no family contains both plant and animal bHLH genes. We suggest that the diversification of bHLH genes is directly linked to the acquisition of multicellularity, and that important diversification of the bHLH repertoire occurred independently in animals and plants.ConclusionsAs the last common ancestor of worm, fly and human is also that of all bilaterian animals, our analysis indicates that this ancient ancestor must have possessed at least 43 different types of bHLH, highlighting its genomic complexity.

| S-EPMC116727 | biostudies-literature

Analysis of helix-helix interactions of bacteriorhodopsin by replica-exchange simulations.

Project description:We performed long-time replica-exchange Monte Carlo simulations of bacteriorhodopsin transmembrane helices, which made it possible that wide conformational space was sampled. Using only the helix-helix interactions and starting from random initial configurations, we obtained the nativelike helix arrangement successfully and predicted a part of the configurations (three helices out of seven) precisely. By the principal component analysis we classified low-energy structures into some clusters of similar structures, and we showed that the above nativelike three-helix configuration is reproduced properly in most clusters and that not only the van der Waals interactions but also the electrostatic interactions contributed to the stabilization of the native structures.

| S-EPMC2716567 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data