BCL::Conf – Improved Open-Source Knowledge-Based Conformation Sampling using the Crystallographic Open Database

2020 ◽  
Author(s):  
Jeffrey Mendenhall ◽  
Benjamin Brown ◽  
Sandeepkumar Kothiwale ◽  
Jens Meiler
Keyword(s):  
Ligand Binding ◽  
Open Source ◽  
Operating Systems ◽  
Generation Algorithm ◽  
Rotamer Library ◽  
Conformer Generation ◽  
Knowledge Based

<div>This paper describes recent improvements made to the BCL::Conf rotamer generation algorithm and comparison of its performance against other freely available and commercial conformer generation software. We demonstrate that BCL::Conf, with the use of rotamers derived from the COD, more effectively recovers crystallographic ligand-binding conformations seen in the PDB than other commercial and freely available software. BCL::Conf is now distributed with the COD-derived rotamer library, free for academic use. The BCL can be downloaded at <a href="http://meilerlab.org/index.php/bclcommons/show/b_apps_id/1">http://meilerlab.org/ bclcommons</a> for Windows, Linux, or Apple operating systems.<br></div>

BCL::Conf – Improved Open-Source Knowledge-Based Conformation Sampling using the Crystallographic Open Database

2020 ◽  
Author(s):  
Jeffrey Mendenhall ◽  
Benjamin Brown ◽  
Sandeepkumar Kothiwale ◽  
Jens Meiler
Keyword(s):  
Ligand Binding ◽  
Open Source ◽  
Operating Systems ◽  
Generation Algorithm ◽  
Rotamer Library ◽  
Conformer Generation ◽  
Knowledge Based

<div>This paper describes recent improvements made to the BCL::Conf rotamer generation algorithm and comparison of its performance against other freely available and commercial conformer generation software. We demonstrate that BCL::Conf, with the use of rotamers derived from the COD, more effectively recovers crystallographic ligand-binding conformations seen in the PDB than other commercial and freely available software. BCL::Conf is now distributed with the COD-derived rotamer library, free for academic use. The BCL can be downloaded at <a href="http://meilerlab.org/index.php/bclcommons/show/b_apps_id/1">http://meilerlab.org/ bclcommons</a> for Windows, Linux, or Apple operating systems.<br></div>

scholarly journals Options for putting CDS/ISIS databases on the internet

2006 ◽  
Vol 40 (3) ◽  
pp. 286-295 ◽  
Author(s):  
Andrew Buxton
Keyword(s):  
Open Source ◽  
Programming Languages ◽  
Operating Systems ◽  
Open Source Software ◽  
Design Methodology ◽  
The Internet ◽  
Content Type

PurposeTo review the variety of software solutions available for putting CDS/ISIS databases on the internet. To help anyone considering which route to take.Design/methodology/approachBriefly describes the characteristics, history, origin and availability of each package. Identifies the type of skills required to implement the package and the kind of application it is suited to. Covers CDS/ISIS Unix version, JavaISIS, IsisWWW, WWWISIS Versions 3 and 5, Genisis, IAH, WWW‐ISIS, and OpenIsis.FindingsThere is no obvious single “best” solution. Several are free but may require more investment in acquiring the skills to install and configure them. The choice will depend on the user's experience with CDS/ISIS formatting language, HTML, programming languages, operating systems, open source software, and so on.Originality/valueThere is detailed documentation available for most of these packages, but little previous guidance to help potential users to distinguish and choose between them.

Open source real-time operating systems for plasma control at FTU

2004 ◽  
Vol 51 (3) ◽  
pp. 476-481 ◽  
Author(s):  
C. Centioli ◽  
F. Iannone ◽  
G. Mazza ◽  
M. Panella ◽  
L. Pangione ◽  
...  
Keyword(s):  
Open Source ◽  
Real Time ◽  
Operating Systems ◽  
Plasma Control

Open Source

2019 ◽  
pp. 1067-1075
Author(s):  
Heidi Lee Schnackenberg
Keyword(s):  
General Population ◽  
Open Source ◽  
Operating Systems ◽  
Open Source Software ◽  
Mobile Applications ◽  
Free Software ◽  
Free Products

The phrase “open source” is not something often heard in everyday conversation. However, the idea of downloadable, free software, particularly mobile applications, or “apps,” has become quite commonplace. Individuals often download free products, grateful that they are available and will potentially work well, without thinking where they originate or why they even exist. Not so long ago, most things associated with computers available to the general population came at a cost and were available from only a few vendors. This is no longer the case thanks to the ever-increasing availability and popularity of open source software, operating systems, and applications.

Open Source Survey Software

2007 ◽  
pp. 273-275 ◽  
Author(s):  
J. Baker
Keyword(s):  
Open Source ◽  
Operating Systems ◽  
Software Design ◽  
Management System ◽  
Online Community ◽  
Course Management System ◽  
The Internet ◽  
Course Management ◽  
Online Surveys ◽  
Software Programs

One of the significant advances in software design afforded by the internet has been the open source movement, an effort to collaboratively create software and make it widely and freely available to the online community. Although the open source movement started with Unix-like computer operating systems, it has expanded to include a wide variety of software programs, including tools to publish and analyze online surveys. This article introduces the open source movement and then profiles three leading open source survey programs: php Easy Survey Package (phpESP), PHP Surveyor, and the Moodle course management system.

Design and Development of Online Course Materials

2009 ◽  
pp. 280-304
Author(s):  
Chao Lee
Keyword(s):  
Instructional Design ◽  
Instructional Technology ◽  
Open Source ◽  
Operating Systems ◽  
Online Course ◽  
Material Development ◽  
Course Materials ◽  
Development Cycle ◽  
Course Material

In the previous chapter, we discussed client computers, desktop operating systems and desktop environments. A desktop environment is the platform where most of the online course materials will be developed. This chapter will focus on course material development with open source technologies. The first part of this chapter is a brief introduction of instructional design and instructional technology theories. We will discuss the development cycle of technology based course materials. The theories of instructional design and instructional technology will be used to guide the development process. After the introduction, we will look at some of the open source tools that can be used to develop online course materials. We will have some detailed discussion on the open source Web authoring, multimedia, and collaboration tools. We will explore the options we may have and the functionalities provided by these open source tools.

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