Download Shareware and Freeware Software for Windows, Linux, Macintosh, PDA

line Home  |  About Us  |  Link To Us  |  FAQ  |  Contact

Serving Software Downloads in 976 Categories, Downloaded 29.545.414 Times

Open3DALIGN for Linux 2.102

Company: Paolo Tosco
Date Added: August 07, 2012  |  Visits: 217

Open3DALIGN for Linux
Full screenshot

Report Broken Link
Printer Friendly Version



Download (41 downloads)



Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is installed on the system while Open3DALIGN is being operated interactively, the setup of alignments can be followed in real time on PyMOL's viewport.

A typical workflow could be the following:

1. A dataset is imported as SDF file
2. Optionally, for each compound of the dataset a quenched molecular dynamics (QMD) conformational search is carried out to find the most stable conformers in a user-defined energy range from the global minimum
3. One or more template compounds are chosen, then the whole dataset is best-aligned to the template(s). The alignment is a performed rigidly, using for each compound of the dataset either the single conformation originally imported or the conformational databases previously obtained by QMD. Additionally, SDF conformational databases can be easily imported from external conformational engines such as MOE and OMEGA. In the latter case, the conformers which best fit the template(s) are chosen out of the conformational pool. Interestingly, conformational flexibility may also be taken into account for templates.
4. Finally, an SDF database constituted by the dataset compounds aligned to each of the templates is obtained

The QMD search is accomplished running a number of short molecular dynamics runs (using the MMFF94 force-field) followed by minimization (using the MMFF94s force-field); these computations are carried out by calling four programs belonging to the TINKER molecular mechanics suite (namely, analyze, dynamic, minimize and optimize) included in Open3DALIGN. MMFF94 atom types are automatically assigned to all compounds of the dataset with the help of SDF2XYZ2SDF, another tool of ours based on OpenBabel.
Alignments are computed in an atom-based fashion (by means of a novel algorithm inspired to the LAMDA algorithm by Richmond and co-workers), in a pharmacophore-based fashion using Pharao as the alignment engine, or finally in a mixed mode consisting in the combination of the latter two methods.
High computational performance is attained splitting the computational tasks over several threads, according to the number of CPUs available in the host running Open3DALIGN.
All computations can be restarted from the point from which they were eventually stopped, allowing most intensive alignment tasks to be completed also in the presence of time-limited computational resources.

Requirements: No special requirements
Release Date: August 07, 2012
Platforms: Linux
Keyword: Alignment Compund Dataset Compound Molecular Alignment Molecular Dynamics Molecule
Users rating: 0/10

License: Freeware Size: 3.3 MB
USER REVIEWS
More Reviews or Write Review


OPEN3DALIGN FOR LINUX RELATED
Multimedia & Graphics  -  Open3DALIGN x64 2.102
Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or...
5.2 MB  
Multimedia & Graphics  -  Open3DALIGN for Mac OS X 2.102
Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or...
3.6 MB  
Multimedia & Graphics  -  Open3DALIGN 2.102
Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or...
4.1 MB  
Education  -  Ascalaph Graphics for Linux 1.0
Ascalaph Graphics is a program for molecular graphics and dynamics, as well as a graphical shell to package of molecular dynamics MDynaMix. Features: Molecular graphics Multiple windows Two cameras per...
16.15 MB  
Multimedia & Graphics  -  BALLView 1.4.0
BALLView is our standalone molecular modeling and visualization application. Furthermore it is also a framework for developing molecular visualization functionality. It is available free of charge under the GPL for Linux, Windows and MacOS. It...
38 MB  
Business  -  Alignment API 3.3
Alignment API is a development tool that allows various ontology matchers to share the same format and interface for accessing matching results. Using ontologies is the privileged way to achieve interoperability among heterogeneous...
32.2 MB  
Multimedia & Graphics  -  Ascalaph Designer 1.8.36
The Ascalaph Designer application was developed for molecular models and simulations. Using this application you can simulate, molecular graphics, optimization, molecular dynamics, quantum chemistry. Features: Molecular graphics Multiple...
72 MB  
Multimedia & Graphics  -  PyMOL 1.4.1
PyMOL is a user-sponsored molecular visualization system on an open-source foundation. Please support development of this open, effective, and affordable software by purchasing an incentive copy, which is pre-built and comes with maintenance and...
9.1 MB  
Multimedia & Graphics  -  PaDEL-Descriptor 2.10
PaDEL-Descriptor is a handy utility designed to perform molecular calculation. It calculates 797 descriptors (663 1D, 2D descriptors and 134 3D descriptors) and 10 types of fingerprints.
 
Modules  -  Image Picker 1.0
Features - Configurable alignment options - Support for Lightbox2 - My Imagepicker tab in My Account - Paging for the image browser - Additional configuration options on the settings page - Upload an image - Automatically generate thumbnails -...
 
NEW DOWNLOADS IN WINDOWS SOFTWARE, MULTIMEDIA & GRAPHICS
Windows Software  -  Movie Box App 3.3.8
Movie Box is Best Application for watching movie, TV shows , Music video, here you to give us clear step by step guide how to download and install Moive Box for Android , all user can free download Movie Box and most user friendly apps. All PC or...
67.23 KB  
Windows Software  -  Cydia Download 1.1.10
This is one of the best freeware released for users. What is Cydia Download ? This is simple downloader which has developed for install Cydia for your device less than ten minutes of time. This freeware is important for all jailbreak users. You...
67.23 KB  
Windows Software  -  Jihosoft iOS10 Backup Extractor 7.0.7
What can you do to extract and recover your iPhone data if you get them lost for the following reasons: 1.Deleted important data from iPhone by mistake. 2.iPhone is damaged, lost or stolen. 3.iPhone stuck in black/white screen of death, iPhone...
16.5 MB  
Windows Software  -  Screenshot Captor 4.15.0
Screenshot Captor is designed for grabbing lots of screenshots with minimal intervention. It has great multimon suport and includes a full image explorer with full shell functionality and unsurpassed integration with external tools like graphic...
7.15 MB  
Windows Software  -  MonitorPack Guard 5.4.1
MonitorPack provides Windows tools at no cost for server monitoring, IT asset management and help Desk solution, optional Cloud Solution (IaaS or Infrastructure as a Service) Cloud Application (Platform as a Service) and software on demand (SaaS...
11.01 MB  
Multimedia & Graphics  -  Pixillion Image Converter Software Free 4.06
Pixillion is a free JPEG and image file format conversion software for Windows. Pixillion Image Converter Software Free can convert files from and to JPEG and other file formats like gif, tiff, png, pdf and more. Before converting your file...
857.73 KB  
Multimedia & Graphics  -  EWD 3D 5.7.5
EWD 3D is a 3D CAD program. The software contains the major CAD functions (line, arc, polyline, spline, face, 3D solid, 3D Surface). Support boolean operation, undo/redo, drag/drop, OSNAP. And have good interactive,easy to use UI. Version EWD...
14.3 MB  
Multimedia & Graphics  -  EasyBanner Free 5.0
EasyBanner Free is free software that makes it easy and simple to create banners in GIF format. The design method is simple and you have the possibility to specify everything in the banner: background, texts, images, styles and animated effects....
2.23 MB  
Multimedia & Graphics  -  Free AVI/MPEG/WMV/MP4/FLV Video Joiner 4.4.5
Free AVI/MPEG/WMV/MP4/FLV Video Joiner, a perfect easy-to-use video joining tool, allows the users to easily and quickly join more than one video file of different formats to one file of a specified format including AVI, MP4, FLV, WMV, etc. The...
6.55 MB  
Multimedia & Graphics  -  Webcam/Screen Video Capture Free 7.5.6
Webcam/Screen Video Capture Free is able to capture video from devices like webcams, IP-cameras, streaming video and more to AVI, MP4, FLV, WMV, MKV, etc., making the quickest and clearest way to communicate reachable for all people. It can record...
4.25 MB