scholarly journals The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects

2020 ◽  
Author(s):  
Alessandro Pedretti ◽  
Angelica Mazzolari ◽  
Silvia Gervasoni ◽  
Laura Fumagalli ◽  
Giulio Vistoli
Keyword(s):  
Drug Design ◽  
Computational Chemistry ◽  
Source Code ◽  
Command Line ◽  
Design Studies ◽  
Non Profit ◽  
Flexible Architecture ◽  
Design Projects ◽  
Technology Level ◽  
Command Line Version

Abstract The purpose of the article is to offer an overview of the latest release of the VEGA suite of programs. This software has been constantly developed and freely released during the last 20 years and has now reached a significant diffusion and technology level as confirmed by the about 22 500 registered users. While being primarily developed for drug design studies, the VEGA package includes cheminformatics and modeling features, which can be fruitfully utilized in various contexts of the computational chemistry. To offer a glimpse of the remarkable potentials of the software, some examples of the implemented features in the cheminformatics field and for structure-based studies are discussed. Finally, the flexible architecture of the VEGA program which can be expanded and customized by plug-in technology or scripting languages will be described focusing attention on the HyperDrive library including highly optimized functions. Availability and implementation: The VEGA suite of programs and the source code of the VEGA command-line version are available free of charge for non-profit organizations at http://www.vegazz.net. Contact: [email protected]

scholarly journals Reconsidering anion inhibitors in the general context of drug design studies of modulators of activity of the classical enzyme carbonic anhydrase

2021 ◽  
Vol 36 (1) ◽  
pp. 561-580 ◽  
Author(s):  
Alessio Nocentini ◽  
Andrea Angeli ◽  
Fabrizio Carta ◽  
Jean-Yves Winum ◽  
Raivis Zalubovskis ◽  
...  
Keyword(s):  
Drug Design ◽  
Carbonic Anhydrase ◽  
General Context ◽  
Design Studies

Fortran90 sources of the subroutines ofUMWEG. III. TheUMWEG-specific subroutines

2007 ◽  
Vol 40 (1) ◽  
pp. 185-187
Author(s):  
Elisabeth Rossmanith
Keyword(s):  
Command Line ◽  
Main Program ◽  
Command Line Version

The Fortran90 sources of theUMWEG-specific subroutines of the programUMWEGare presented and deposited, together with the PostScript-plot software subroutines and the simple and short main program of the command-line version of the programUMWEG.

scholarly journals Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files

2015 ◽  
Vol 14 ◽  
pp. CIN.S26470 ◽  
Author(s):  
Richard P. Finney ◽  
Qing-Rong Chen ◽  
Cu V. Nguyen ◽  
Chih Hao Hsu ◽  
Chunhua Yan ◽  
...  
Keyword(s):  
Graphical User Interface ◽  
Reference Genome ◽  
Source Code ◽  
Software Tool ◽  
Command Line ◽  
Sequencing Data ◽  
Genome Data ◽  
Command Line Tool ◽  
Portable Software ◽  
Microsoft Windows

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview . The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview .

scholarly journals Vargas: heuristic-free alignment for assessing linear and graph read aligners

2019 ◽  
Author(s):  
Charlotte A. Darby ◽  
Ravi Gaddipati ◽  
Michael C. Schatz ◽  
Ben Langmead
Keyword(s):  
Gold Standard ◽  
Source Code ◽  
Alignment Accuracy ◽  
Local Alignment ◽  
Maximum Speed ◽  
Command Line ◽  
Scoring Functions ◽  
Large Numbers ◽  
Computationally Intensive ◽  
Optimal Alignments

AbstractRead alignment is central to many aspects of modern genomics. Most aligners use heuristics to accelerate processing, but these heuristics can fail to find the optimal alignments of reads. Alignment accuracy is typically measured through simulated reads; however, the simulated location may not be the (only) location with the optimal alignment score. Vargas implements a heuristic-free algorithm guaranteed to find the highest-scoring alignment for real sequencing reads to a linear or graph genome. With semiglobal and local alignment modes and affine gap and quality-scaled mismatch penalties, it can implement the scoring functions of commonly used aligners to calculate optimal alignments. While this is computationally intensive, Vargas uses multi-core parallelization and vectorized (SIMD) instructions to make it practical to optimally align large numbers of reads, achieving a maximum speed of 456 billion cell updates per second. We demonstrate how these “gold standard” Vargas alignments can be used to improve heuristic alignment accuracy by optimizing command-line parameters in Bowtie 2, BWA-MEM, and vg to align more reads correctly. Source code implemented in C++ and compiled binary releases are available at https://github.com/langmead-lab/vargas under the MIT license.

scholarly journals idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates

2020 ◽  
Author(s):  
Xun Zhu ◽  
Ti-Cheng Chang ◽  
Richard Webby ◽  
Gang Wu
Keyword(s):  
Personal Computer ◽  
Source Code ◽  
Command Line ◽  
Sequencing Data ◽  
Link Type ◽  
Public Dataset ◽  
Virus Isolates

AbstractidCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Using a public dataset, we show that idCOV can make equivalent calls as annotated by Nextstrain.org on all three common clade systems using user uploaded FastQ files directly. Web and equivalent command-line interfaces are available. It can be deployed on any Linux environment, including personal computer, HPC and the cloud. The source code is available at https://github.com/xz-stjude/idcov. A documentation for installation can be found at https://github.com/xz-stjude/idcov/blob/master/README.md.

scholarly journals The UCSC Genome Browser database: 2018 update

2017 ◽  
Vol 46 (D1) ◽  
pp. D762-D769 ◽  
Author(s):  
Jonathan Casper ◽  
Ann S Zweig ◽  
Chris Villarreal ◽  
Cath Tyner ◽  
Matthew L Speir ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Gene Interactions ◽  
Command Line ◽  
Web Interface ◽  
Variant Annotation ◽  
The Past ◽  
Ucsc Genome Browser Database ◽  
Genome Assemblies ◽  
Command Line Version

Abstract The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis—12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.

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