Open3DALIGN for Mac OS X 2.28

Paolo Tosco in Graphic Apps / CAD

Open3DALIGN for Mac OS X screenshot

User Rating: 2.5 (15 votes)

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.

File Size: 3.599609375 MB License: Freeware Price: FREE
Platform: Mac OS X
Downloads: Total: 138 | This Month: 15 Released: 2014-11-20
Open3DALIGN for Mac OS X Similar Software

Circuitscape for Mac OS X 4.0.5 Brad McRae & Viral B. Shah    

... across a landscape simultaneously. We are developing Circuitscape for Mac OS X, Windows, and Linux. .... Free download of Circuitscape for Mac OS X 4.0.5

software pick   

LayoutEditor for Mac OS X 20170428 Jürgen Thies    

... is a program to design and edit layouts for MEMS/IC fabrication. As well as it is suitably for Multi-Chip-Modules (MCM), Chip-on-Board (COB), Low temperature co-fired ceramics ... is crossplatform compatible and runs on Windows, Linux, Mac OS X and much more platforms. .... Free download of LayoutEditor for Mac OS X 20170428

software pick   

Gnuplot for Mac OS X 4.6.4 Philipp K. Janert    

Gnuplot is a portable command-line driven graphing utility for linux, OS/2, MS Windows, OSX, VMS, and many ... freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists ... on wxWidgets and the creation of mousable graphs for web display using the HTML5 canvas element. .... Free download of Gnuplot for Mac OS X 4.6.4

software pick   

FidoCadJ for Mac OS X 0.24.6 Davide Bucci    

... is a very immediate and effective EDA tool for the hobbyst. FidoCadJ stores its drawings in ... compact text format. This choice is well suited for the copy and paste in newsgroups and forums. ... · Easy to use · Compact text format, for copy/pasting in Usenet messages · FidoCad compatible .... Free download of FidoCadJ for Mac OS X 0.24.6

software pick   

LigandScout for Mac OS X 3.12 Ligand    

LigandScout 3.0 is a fully integrated platform for accurate virtual screening based on 3D chemical feature ... modeling, and includes novel high performance alignment algorithms for excellent prediction quality with unprecedented screening speed. Additionally, ... tools, including the automated generation of ROC curves for performance assessments. All functions are accessible through ... · Pharmacophore export to Catalyst, MOE and Phase for virtual screening · Extensive parameter control for more .... Free download of LigandScout for Mac OS X 3.12

software pick   
Popular Software in Graphic Apps / CAD

Proteus PCB Design 8.6 SP3 B23669 Labcenter Electronics Ltd.    

A powerful application for circuit board designers. Free download of Proteus PCB Design 8.6 SP3 B23669

MaxIm DL 5.24 Diffraction Limited    

A comprehensive astronomical manager and photo editor. Free download of MaxIm DL 5.24

software pick   

SmartSignSafety -- Visual Digital Signature For AutoCAD 3.0 SummerCAD    

In case of modification of the drawing, the signature disappears immediately.. Free download of SmartSignSafety -- Visual Digital Signature For AutoCAD 3.0

LispLink 2010 CAE-Link Corporation    

An advanced text editor that allows you to use all AutoCAD customization files. Free download of LispLink 2010

software pick   

SWLibrary 1.2.0 Vladimir Galouchko    

Create 3D contour surface. The library with source code.. Free download of SWLibrary 1.2.0