scholarly journals MoMA-LoopSampler: A web server to exhaustively sample protein loop conformations

2021 ◽  
Author(s):  
Amélie Barozet ◽  
Kevin Molloy ◽  
Marc Vaisset ◽  
Christophe Zanon ◽  
Pierre Fauret ◽  
...  
Keyword(s):  
Sampling Method ◽  
Geometric Constraints ◽  
Conformational Space ◽  
Supplementary Information ◽  
Use Case ◽  
Supplementary Data ◽  
Sampling Process ◽  
Loop Conformations ◽  
Intensive Use ◽  
Flexible Protein

Abstract Summary MoMA-LoopSampler is a sampling method that globally explores the conformational space of flexible protein loops. It combines a large structural library of three-residue fragments and a novel reinforcement-learning-based approach to accelerate the sampling process while maintaining diversity. The method generates a set of statistically-likely loop states satisfying geometric constraints, and its ability to sample experimentally observed conformations has been demonstrated. This paper presents a web user interface to MoMA-LoopSampler through the illustration of a typical use-case. Availability MoMA-LoopSampler is freely available at: https://moma.laas.fr/applications/LoopSampler/ We recommend users to create an account, but anonymous access is possible. In most cases, jobs are completed within a few minutes. The waiting time may increase depending on the server load, but it very rarely exceeds an hour. For users requiring more intensive use, binaries can be provided upon request. Supplementary information Supplementary data are available at Bioinformatics online.

Increasing the accuracy of protein loop structure prediction with evolutionary constraints

2018 ◽  
Vol 35 (15) ◽  
pp. 2585-2592 ◽  
Author(s):  
Claire Marks ◽  
Charlotte M Deane
Keyword(s):  
Structure Prediction ◽  
De Novo ◽  
Conformational Space ◽  
Supplementary Information ◽  
Evolutionary Constraints ◽  
Final Model ◽  
Loop Conformations ◽  
Loop Regions ◽  
Accuracy Of Prediction ◽  
Protein Models

Abstract Motivation Accurate prediction of loop structures remains challenging. This is especially true for long loops where the large conformational space and limited coverage of experimentally determined structures often leads to low accuracy. Co-evolutionary contact predictors, which provide information about the proximity of pairs of residues, have been used to improve whole-protein models generated through de novo techniques. Here we investigate whether these evolutionary constraints can enhance the prediction of long loop structures. Results As a first stage, we assess the accuracy of predicted contacts that involve loop regions. We find that these are less accurate than contacts in general. We also observe that some incorrectly predicted contacts can be identified as they are never satisfied in any of our generated loop conformations. We examined two different strategies for incorporating contacts, and on a test set of long loops (10 residues or more), both approaches improve the accuracy of prediction. For a set of 135 loops, contacts were predicted and hence our methods were applicable in 97 cases. Both strategies result in an increase in the proportion of near-native decoys in the ensemble, leading to more accurate predictions and in some cases improving the root-mean-square deviation of the final model by more than 3 Å. Supplementary information Supplementary data are available at Bioinformatics online.

HaploGrouper: a generalized approach to haplogroup classification

2020 ◽  
Author(s):  
Anuradha Jagadeesan ◽  
S Sunna Ebenesersdóttir ◽  
Valdis B Guðmundsdóttir ◽  
Elisabet Linda Thordardottir ◽  
Kristjan H S Moore ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Tree ◽  
Y Chromosome ◽  
State Of The Art ◽  
Supplementary Information ◽  
Sequence Variants ◽  
Use Case ◽  
Supplementary Data ◽  
Human Mitochondrial Dna ◽  
Comparable Accuracy

Abstract Motivation We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans. Results HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species—given an extant annotated phylogenetic tree defined by sequence variants. Availability and implementation The software is available at the following URL https://gitlab.com/bio_anth_decode/haploGrouper. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals DNA Features Viewer: a sequence annotation formatting and plotting library for Python

2020 ◽  
Vol 36 (15) ◽  
pp. 4350-4352 ◽  
Author(s):  
Valentin Zulkower ◽  
Susan Rosser
Keyword(s):  
Computational Biology ◽  
Open Source ◽  
Programming Language ◽  
Source Code ◽  
Supplementary Information ◽  
Use Case ◽  
Sequence Annotation ◽  
Supplementary Data ◽  
Python Programming Language ◽  
Python Programming

Abstract Motivation Although the Python programming language counts many Bioinformatics and Computational Biology libraries; none offers customizable sequence annotation visualizations with layout optimization. Results DNA Features Viewer is a sequence annotation plotting library which optimizes plot readability while letting users tailor other visual aspects (colors, labels, highlights etc.) to their particular use case. Availability and implementation Open-source code and documentation are available on Github under the MIT license (https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer). Supplementary information Supplementary data are available at Bioinformatics online.

Pengaruh Citra Merek, Kualitas Produk Dan Harga Terhadap Kepuasan Konsumen Pada Bisnis Franchise Minuman

2017 ◽  
Vol 24 (2) ◽  
pp. 144-153
Author(s):  
Yunita Fitri Wahyuningtyas
Keyword(s):  
Regression Analysis ◽  
Marketing Strategy ◽  
Product Quality ◽  
Multiple Regression Analysis ◽  
Multiple Regression ◽  
Sampling Method ◽  
Sampling Technique ◽  
Sampling Process ◽  
And Function ◽  
Simultaneous Influence

This research is conducted upon the emergence of many companies producing the same product of the same kind and function. It leads to the urgency of proper and well planned marketing strategy. This research aims to investigate how far the influence of branding, product quality, and price toward consumer’s satisfaction in beverage franchise business. This research utilizes 5 likert scale questionnaire which is tested by using multiple regression analysis to reveal whether or not there is partial and simultaneous influence of branding, product quality, and price toward consumer’s satisfaction in beverage franchise business. Sampling method is accidental sampling technique, in which sample of particular population is taken based on the accessibility and availability of the sample during the sampling process. Sample used is 100 samples among consumers or customers of Mang Endy Milkshake. The result shows that branding, product quality, and price influence consumer’s satisfaction in beverage franchise business.

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Epidemiological modeling in StochSS Live!

2021 ◽  
Author(s):  
Richard Jiang ◽  
Bruno Jacob ◽  
Matthew Geiger ◽  
Sean Matthew ◽  
Bryan Rumsey ◽  
...  
Keyword(s):  
Stochastic Model ◽  
Epidemiological Model ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Based ◽  
Epidemiological Modeling ◽  
Modeling Simulation ◽  
Wide Range ◽  
Biochemical Systems

Abstract Summary We present StochSS Live!, a web-based service for modeling, simulation and analysis of a wide range of mathematical, biological and biochemical systems. Using an epidemiological model of COVID-19, we demonstrate the power of StochSS Live! to enable researchers to quickly develop a deterministic or a discrete stochastic model, infer its parameters and analyze the results. Availability and implementation StochSS Live! is freely available at https://live.stochss.org/ Supplementary information Supplementary data are available at Bioinformatics online.

KEC: unique sequence search by K-mer exclusion

2021 ◽  
Author(s):  
Pavel Beran ◽  
Dagmar Stehlíková ◽  
Stephen P Cohen ◽  
Vladislav Čurn
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Source Code ◽  
Unique Sequence ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Laptop Computers ◽  
Sequence Search ◽  
Target Sequences ◽  
Cross Reference

Abstract Summary Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications. Availability and implementation KEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

2020 ◽  
Author(s):  
Matteo Chiara ◽  
Federico Zambelli ◽  
Marco Antonio Tangaro ◽  
Pietro Mandreoli ◽  
David S Horner ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Ad Hoc ◽  
State Of The Art ◽  
Supplementary Information ◽  
Genomic Sequences ◽  
Supplementary Data ◽  
Evolutionary Patterns ◽  
Genomic Variants ◽  
Art Methods ◽  
Available Resources

Abstract Summary While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2. Availabilityand implementation Galaxy   http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals UniBioDicts: Unified access to Biological Dictionaries

2020 ◽  
Author(s):  
John Zobolas ◽  
Vasundra Touré ◽  
Martin Kuiper ◽  
Steven Vercruysse
Keyword(s):  
User Interface ◽  
Life Science ◽  
Biological Data ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Query Interface ◽  
Controlled Vocabularies ◽  
Search String ◽  
Software Packages ◽  
The Right

Abstract Summary We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts or UBDs) provide a single query-interface for accessing the online API services of leading biological data providers. Given a search string, UBDs return a list of matching term, identifier and metadata units from databases (e.g. UniProt), controlled vocabularies (e.g. PSI-MI) and ontologies (e.g. GO, via BioPortal). This functionality can be connected to input fields (user-interface components) that offer autocomplete lookup for these dictionaries. UBDs create a unified gateway for accessing life science concepts, helping curators find annotation terms across resources (based on descriptive metadata and unambiguous identifiers), and helping data users search and retrieve the right query terms. Availability and implementation The UBDs are available through npm and the code is available in the GitHub organisation UniBioDicts (https://github.com/UniBioDicts) under the Affero GPL license. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CONCUR: quick and robust calculation of codon usage from ribosome profiling data

2020 ◽  
Author(s):  
Michaela Frye ◽  
Susanne Bornelöv
Keyword(s):  
Codon Usage ◽  
Ribosome Profiling ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Usage Analysis

Abstract Summary CONCUR is a standalone tool for codon usage analysis in ribosome profiling experiments. CONCUR uses the aligned reads in BAM format to estimate codon counts at the ribosome E-, P- and A-sites and at flanking positions. Availability and implementation CONCUR is written in Perl and is freely available at https://github.com/susbo/concur. Supplementary information Supplementary data are available at Bioinformatics online.

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