CueMol 2.2.3.443 – Macromolecular Structure Visualization

CueMol 2.2.3.443

:: DESCRIPTION

CueMol is a computer program for the macromolecular structure visualization (CueMol was formerly called “Que”). CueMol aims to visualize the crystallographic models of macromolecules with the user-friendly interfaces. Currently supported files are molecular coordinates (PDB format), electron density (CCP4, CNS , and BRIX formats), MSMS surface data, and GRASP and APBS electrostatic potential map.

::DEVELOPER

Dr. Ryuichiro Ishitani

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ MacOsX / iOS

:: DOWNLOAD

CueMol , for iOS

:: MORE INFORMATION

Theseus 3.3.0 – Superimpose Macromolecular Structures

Theseus 3.3.0

:: DESCRIPTION

Theseus is a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood. By downweighting variable regions of the superposition and by correcting for correlations among atoms, the ML superpositioning method produces much more accurate results.

When superpositioning macromolecules with different residue sequences, other programs and algorithms discard residues that are aligned with gaps. Theseus, however, uses a novel maximum likelihood superposition algorithm that includes all of the data.

::DEVELOPER

Douglas Theobald <dtheobald@brandeis.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 Theseus

:: MORE INFORMATION

Citation

Theobald, Douglas L. & Wuttke, Deborah S. (2006b)
THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures.
Bioinformatics 22(17):2171-2172

MAXIT 8.120 – An application for Processing and Annotating of Macromolecular Structure data

MAXIT 8.120

:: DESCRIPTION

The Maxit Program Suite was developed by the PDB (Protein Data Bank) and NDB (Nucleic Acid Database) to assist in the processing and curation of macromolecular structure data.

::DEVELOPER

RCSB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MAXIT, Source Code

:: MORE INFORMATION

GRASP 2 -Visualization of Macromolecular Structures and Sequences

GRASP 2

:: DESCRIPTION

GRASP (Graphical Representation and Analysis of Structural Properties) is a program used for macromolecular structure and surface visualization. It contains a large number of new features and scientific tools: Enhanced GUI; Structure alignment and domain database scanning; A gaussian surface generator and new surface coloring schemes; Sequence visualization and alignment; Completed work can be stored in project files; Among the many objects that can be stored in a project file are views of the structure; defined subsets, surfaces; Direct printing to printers at full printer resolution.

::DEVELOPER

Barry Honig’s group 

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GRASP

:: MORE INFORMATION

Citation

Petrey, D. and Honig, B. (2003)
GRASP2: Visualization, Surface Properties, and Electrosttics of Macromolecular Structures and Sequences.
Methods in Enzymology. 374: 492-509

BioEditor 1.6.1 – Present Macromolecular Structure & Structural Annotation

BioEditor 1.6.1

:: DESCRIPTION

BioEditor is a tool to bridge the gap between the printed literature and current Internet presentation formats. It is a standalone Windows application that can be used to prepare and present structure annotations containing formatted text, graphics, sequence data, and interactive molecular views. This presentation will summarize the features of BioEditor and provide an overview of a series of annotations that have been developed on DNA-protein complexes.

::DEVELOPER

Peng Yang, Paul A. Craig, Philip E. Bourne, David Goodsell, San Diego Supercomper Center

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BioEditor

:: MORE INFORMATION

N/A