scholarly journals GAPIN: Grouped and Aligned Protein Interface Networks

2019 ◽  
Author(s):  
Biharck M. Araújo ◽  
Aline L. Coelho ◽  
Sabrina A. Silveira ◽  
João P. R. Romanelli ◽  
Raquel C. de Melo-Minardi ◽  
...  
Keyword(s):  
Interaction Network ◽  
Supplementary Information ◽  
Protein Interface ◽  
Supplementary Data ◽  
Web Interface ◽  
Web Based ◽  
Structural Interaction ◽  
Peptidase Inhibitor ◽  
Supplementary Material ◽  
Hydrophobic Patterns

AbstractSummaryGAPIN is a web-based application for structural interaction network analysis among any type of PDB molecules, regardless of whether their interfaces are between chain-chain or chain-ligand. A special emphasis is given to graph clustering, allowing users to scrutinize target contexts for ligand candidates. We show how GAPIN can be used to unveil underlying hydrophobic patterns on a set of peptidase-inhibitor complexes. In another experiment, we show there is a positive correlation between cluster sizes and the presence of druggable spots, indicating that the clustering may discriminate the higher complexity of these hot subnetworks.Availability and implementationGAPIN is freely available as an easy-to-use web interface at https://[email protected], [email protected] informationSupplementary data are available online.

scholarly journals EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening

2020 ◽  
Vol 36 (14) ◽  
pp. 4200-4202 ◽  
Author(s):  
Douglas E V Pires ◽  
Wandré N P Veloso ◽  
YooChan Myung ◽  
Carlos H M Rodrigues ◽  
Michael Silk ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Interface ◽  
Web Based ◽  
Protein Target ◽  
User Friendly ◽  
Library Selection ◽  
Intuitive Interface

Abstract Summary EasyVS is a web-based platform built to simplify molecule library selection and virtual screening. With an intuitive interface, the tool allows users to go from selecting a protein target with a known structure and tailoring a purchasable molecule library to performing and visualizing docking in a few clicks. Our system also allows users to filter screening libraries based on molecule properties, cluster molecules by similarity and personalize docking parameters. Availability and implementation EasyVS is freely available as an easy-to-use web interface at http://biosig.unimelb.edu.au/easyvs. Contact [email protected] or [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

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.

scholarly journals BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications

2018 ◽  
Vol 35 (14) ◽  
pp. 2518-2520
Author(s):  
Adrián Bazaga ◽  
Alfonso Valencia ◽  
María- JoséRementeria
Keyword(s):  
General Public ◽  
Fast Growth ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Based ◽  
Research Publications

Abstract Motivation The fast growth of bioinformatics adds a significant difficulty to assess the contribution, geographical and thematic distribution of the research publications. Results To help researchers, grant agencies and general public to assess the progress in bioinformatics, we have developed BIOLITMAP, a web-based geolocation system that allows an easy and sensible exploration of the publications by institution, year and topic. Availability and implementation BIOLITMAP is available at http://socialanalytics.bsc.es/biolitmap and the sources have been deposited at https://github.com/inab/BIOLITMAP. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals INDRA-IPM: interactive pathway modeling using natural language with automated assembly

2019 ◽  
Vol 35 (21) ◽  
pp. 4501-4503 ◽  
Author(s):  
Petar V Todorov ◽  
Benjamin M Gyori ◽  
John A Bachman ◽  
Peter K Sorger
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Web Service ◽  
Language Processing ◽  
Source Code ◽  
Supplementary Information ◽  
Expression Data ◽  
Supplementary Data ◽  
Automated Assembly ◽  
Web Based

Abstract Summary INDRA-IPM (Interactive Pathway Map) is a web-based pathway map modeling tool that combines natural language processing with automated model assembly and visualization. INDRA-IPM contextualizes models with expression data and exports them to standard formats. Availability and implementation INDRA-IPM is available at: http://pathwaymap.indra.bio. Source code is available at http://github.com/sorgerlab/indra_pathway_map. The underlying web service API is available at http://api.indra.bio:8000. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Crosslink: A fast, scriptable genetic mapper for outcrossing species

2017 ◽  
Author(s):  
Robert J. Vickerstaff ◽  
Richard J. Harrison
Keyword(s):  
Large Datasets ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Link Type ◽  
Mapping Software ◽  
Outcrossing Species ◽  
Supplementary Material ◽  
Novel Approaches ◽  
Similar Accuracy ◽  
General Public License

AbstractSummaryCrosslink is genetic mapping software for outcrossing species designed to run efficiently on large datasets by combining the best from existing tools with novel approaches. Tests show it runs much faster than several comparable programs whilst retaining a similar accuracy.Availability and implementationAvailable under the GNU General Public License version 2 from https://github.com/eastmallingresearch/[email protected] informationSupplementary data are available at Bioinformatics online and from https://github.com/eastmallingresearch/crosslink/releases/tag/v0.5.

scholarly journals Reconstructing signaling pathways using regular language constrained paths

2019 ◽  
Vol 35 (14) ◽  
pp. i624-i633 ◽  
Author(s):  
Mitchell J Wagner ◽  
Aditya Pratapa ◽  
T M Murali
Keyword(s):  
Signaling Pathways ◽  
Regular Language ◽  
Interaction Network ◽  
Automated Analysis ◽  
Supplementary Information ◽  
Natural Question ◽  
Supplementary Data ◽  
High Quality ◽  
Alternative Approaches ◽  
New Interactions

Abstract Motivation High-quality curation of the proteins and interactions in signaling pathways is slow and painstaking. As a result, many experimentally detected interactions are not annotated to any pathways. A natural question that arises is whether or not it is possible to automatically leverage existing pathway annotations to identify new interactions for inclusion in a given pathway. Results We present RegLinker, an algorithm that achieves this purpose by computing multiple short paths from pathway receptors to transcription factors within a background interaction network. The key idea underlying RegLinker is the use of regular language constraints to control the number of non-pathway interactions that are present in the computed paths. We systematically evaluate RegLinker and five alternative approaches against a comprehensive set of 15 signaling pathways and demonstrate that RegLinker recovers withheld pathway proteins and interactions with the best precision and recall. We used RegLinker to propose new extensions to the pathways. We discuss the literature that supports the inclusion of these proteins in the pathways. These results show the broad potential of automated analysis to attenuate difficulties of traditional manual inquiry. Availability and implementation https://github.com/Murali-group/RegLinker. Supplementary information Supplementary data are available at Bioinformatics online.

SolupHred: a server to predict the pH-dependent aggregation of intrinsically disordered proteins

2020 ◽  
Author(s):  
Carlos Pintado ◽  
Jaime Santos ◽  
Valentín Iglesias ◽  
Salvador Ventura
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Solution Ph ◽  
Predictive Tool ◽  
Web Based ◽  
Intrinsically Disordered ◽  
Dependent Protein ◽  
Ph Dependent

Abstract Summary Polypeptides are exposed to changing environmental conditions that modulate their intrinsic aggregation propensities. Intrinsically disordered proteins (IDPs) constitutively expose their aggregation determinants to the solvent, thus being especially sensitive to its fluctuations. However, solvent conditions are often disregarded in computational aggregation predictors. We recently developed a phenomenological model to predict IDPs' solubility as a function of the solution pH, which is based on the assumption that both protein lipophilicity and charge depend on this parameter. The model anticipated solubility changes in different IDPs accurately. In this application note, we present SolupHred, a web-based interface that implements the aforementioned theoretical framework into a predictive tool able to compute IDPs aggregation propensities as a function of pH. SolupHred is the first dedicated software for the prediction of pH-dependent protein aggregation. Availability and implementation The SolupHred web server is freely available for academic users at: https://ppmclab.pythonanywhere.com/SolupHred. It is platform-independent and does not require previous registration. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals FQSqueezer: k-mer-based compression of sequencing data

2019 ◽  
Author(s):  
Sebastian Deorowicz
Keyword(s):  
Data Compression ◽  
State Of The Art ◽  
Genomic Data ◽  
General Purpose ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Sequencing Data ◽  
Partial Matching ◽  
Supplementary Material ◽  
Better Than

AbstractMotivationThe amount of genomic data that needs to be stored is huge. Therefore it is not surprising that a lot of work has been done in the field of specialized data compression of FASTQ files. The existing algorithms are, however, still imperfect and the best tools produce quite large archives.ResultsWe present FQSqueezer, a novel compression algorithm for sequencing data able to process single- and paired-end reads of variable lengths. It is based on the ideas from the famous prediction by partial matching and dynamic Markov coder algorithms known from the general-purpose-compressors world. The compression ratios are often tens of percent better than offered by the state-of-the-art tools.Availability and Implementationhttps://github.com/refresh-bio/[email protected] informationSupplementary data are available at publisher’s Web site.

scholarly journals GTShark: Genotype compression in large project

2018 ◽  
Author(s):  
Sebastian Deorowicz ◽  
Agnieszka Danek
Keyword(s):  
Web Site ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Link Type ◽  
Large Project ◽  
Supplementary Material

AbstractSummaryNowadays large sequencing projects handle tens of thousands of individuals. The huge files summarizing the findings definitely require compression. We propose a tool able to compress large collections of genotypes as well as single samples in such projects to sizes not achievable to date.Availability and Implementationhttps://github.com/refresh-bio/[email protected] informationSupplementary data are available at publisher’s Web site.

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