CrystalMaker 9.2.5 – Build Crystal & Molecular Structures

CrystalMaker 9.2.5

:: DESCRIPTION

CrystalMaker is a program for building, displaying and manipulating all kinds of crystal and molecular structures.

::DEVELOPER

CrystalMaker Software Limited

:: SCREENSHOTS

CrystalMaker

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 CrystalMaker

:: MORE INFORMATION

Chemozart 1.0 – Web-based 3D Molecular Structure Editor and Visualizer Platform

Chemozart 1.0

:: DESCRIPTION

Chemozart is a web-based 3d molecule editor and visualization platfrom.

::DEVELOPER

Mohamad Mohebifar

:: SCREENSHOTS

Chemozart

:: REQUIREMENTS

  • Web browser
  • JS

:: DOWNLOAD

 Chemozart

:: MORE INFORMATION

Citation

Chemozart: a web-based 3D molecular structure editor and visualizer platform.
Mohebifar M, Sajadi F.
J Cheminform. 2015 Nov 19;7:56. eCollection 2015.

MOLE 2.0 – Location and Characterization of Channels, Tunnels and Pores in Molecular Structures

MOLE 2.0

:: DESCRIPTION

Program MOLE is an universal toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in molecular structures. The core of MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. MOLE is a powerful software (overcomming some limitations of CAVER tool) for exploring large molecular channels, complex networks of channels and molecular dynamics trajectories (AMBER ascii traj and parm7 are supported) in which analysis of a large number of snapshots is required.

::DEVELOPER

Martin Petrek (NCBR), Michal Otyepka (FCH UPOL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

MOLE

:: MORE INFORMATION

Citation:

Structure. 2007 Nov;15(11):1357-63.
MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.
Petrek M, Kosinová P, Koca J, Otyepka M.

XCrySDen 1.5.60 – Crystalline & Molecular Structure Visualisation

XCrySDen 1.5.60

:: DESCRIPTION

XCrySDen (Crystalline Structures and Densities  under the X-Window environment.) is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.

::DEVELOPER

Anton Kokalj

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window with Cygwin

:: DOWNLOAD

 XCrySDen

:: MORE INFORMATION

Citation:

A. Kokalj,
Computer graphics and graphical user interfaces as tools in simulations of matter at the atomic scale
Comp. Mater. Sci., 2003, Vol. 28, p. 155.

WebChem Viewer 1.2.7 – Sharing Molecular Structures and Associated Chemical Information

WebChem Viewer 1.2.7

:: DESCRIPTION

WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed in any modern web browser, on any operating system (including mobile), without requiring the installation of additional software. The output can also be easily incorporated into existing web pages.

::DEVELOPER

Jacob Durrant, @  the lab of Rommie E. Amaro.

:: SCREENSHOTS

WebChemViewer

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 WebChem Viewer 

:: MORE INFORMATION

MOLGEN 5.0 – Molecular Structure Generation

MOLGEN 5.0

:: DESCRIPTION

The program system MOLGEN is devoted to generating all structures (connectivity isomers, constitutions) that correspond to a given molecular formula, with optional further restrictions, e.g. presence or absence of particular substructures. The project arose in 1985 from the idea to provide an efficient and portable tool for molecular structure elucidation in chemical industry, research, and education.

::DEVELOPER

MOLGEN Team

:: SCREENSHOTS

MOLGEN

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 MOLGEN

:: MORE INFORMATION

R. Gugisch, A. Kerber, A. Kohnert, R. Laue, M. Meringer, C. Rücker, A. Wassermann :
MOLGEN 5.0, a Molecular Structure Generator.
Submitted to Bentham Science Publishers Ltd. 2012

CN3D 4.3.1 – 3D Molecular Structure Viewer

CN3D 4.3.1

:: DESCRIPTION

Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI’s Entrez retrieval service. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.

What sets Cn3D apart from other software is its ability to correlate structure and sequence information: for example, a scientist can quickly find the residues in a crystal structure that correspond to known disease mutations, or conserved active site residues from a family of sequence homologs. Cn3D displays structure-structure alignments along with their structure-based sequence alignments, to emphasize what regions of a group of related proteins are most conserved in structure and sequence.

Cn3D reads only data files from the MMDB database, not PDB formatted records.

::DEVELOPER

The NCBI Structure Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Macintosh/Unix/Linux

:: DOWNLOAD

CN3D

:: MORE INFORMATION

Below is a complete list (with links into Entrez) of all literature cited in the preparation of this tutorial.

  1. Di Cristofano A, Pandolfi PP. The multiple roles of PTEN in tumor suppression. Cell 2000 Feb 18; 100(4):387-90. (Entrez)
  2. Lee JO, Yang H, Georgescu MM, Di Cristofano A, Maehama T, Shi Y, Dixon JE, Pandolfi P, Pavletich NP. Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association. Cell 1999 Oct 29; 99(3):323-34. (Entrez)
  3. Liaw D, Marsh DJ, Li J, Dahia PL, Wang SI, Zheng Z, Bose S, Call KM, Tsou HC, Peacocke M, Eng C, Parsons R. Germline mutations of the PTEN gene in Cowden disease, an inherited breast and thyroid cancer syndrome. Nat Genet. 1997 May; 16(1):64-7. (Entrez)

JChemPaint 3.3-1210 – Editor for 2D Molecular Structures

JChemPaint 3.3-1210

:: DESCRIPTION

JChemPaint (or JCP ) is the editor and viewer for 2D chemical structures developed using CDK. It is implemented in several forms: a Java application and two varieties of Java applet.

::DEVELOPER

Steinbeck group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

JChemPaint

:: MORE INFORMATION

Citation:

JChemPaint – Using the Collaborative Forces of the Internet to Develop a Free Editor for 2D Chemical Structures
Stefan Krause, Egon Willighagen and Christoph Steinbeck.
Molecules 5, 93-98 (2000).

ViewMol3D 5.00.alpha.3 – 3D OpenGL Viewer for Molecular Structures

ViewMol3D 5.00.alpha.3

:: DESCRIPTION

ViewMol3D is a 3D OpenGL viewer for molecular structures from the output of quantum chemistry calculations.

::DEVELOPER

Andrew Ryzhkov and Arcady Antipin

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows
  • OpenGL
  • FLTK

:: DOWNLOAD

 ViewMol3D

:: MORE INFORMATION

 

COSMOS 5.0 / COSMOS Viewer 3.0 – Computer Simulation & Visualisation of Molecular Structures

COSMOS 5.0 / COSMOS Viewer 3.0

:: DESCRIPTION

COSMOS is the advanced software package for PC that integrates modeling, crystallography and NMR spectroscopy.

COSMOS Viewer is a freeware product for presentation of molecules. It works with files in COSMOS (*.coo) -format und files in the PDB – Protein Data Bank (*.pdb,*.ent), HYPERCHEM (*.hin), SYBYL (*.mo2), SHELX (*.res, *.ins), GAUSSIAN94,98 (*.out, *.log) and INSIGHT (*.car) format. You can use various styles for graphic representation like stick model, ball-stick model and CPK model, stereo and perspective representation. You can also messure the geometry like distances and angles and perform some calculation tools.

::DEVELOPER

COSMOS Software

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

COSMOSCOSMOS Viewer

:: MORE INFORMATION

N/A