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.
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.
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.
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.
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.
Below is a complete list (with links into Entrez) of all literature cited in the preparation of this tutorial.
Di Cristofano A, Pandolfi PP. The multiple roles of PTEN in tumor suppression. Cell 2000 Feb 18; 100(4):387-90. (Entrez)
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)
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)