MMB 2.19 – Model the Structure and Dynamics of Macromolecules

MMB 2.19

:: DESCRIPTION

MMB (a contraction of MacroMolecule Builder) was previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein as well as RNA. Aside from the renaming, MMB 2.3 differs from RNABuilder 2.2 in two important ways. Release 2.3 has fully overhauled guts. It uses the BiopolymerClassContainer, a much cleaner programming construct which will make future upgrades and extensions more efficient. As of release 2.3.4, we link against new Molmodel binaries which have more efficient tracking of atoms in rigid regions. This yields a two-fold speed improvement and four-fold lower memory requirement for many problems. Also in this release, some rarely used features have been removed, but these were never in the tutorial literature so their absence should go largely unnoticed. The default input file name is now commands.dat rather than contacts.dat. A couple of somewhat obscure bugs were fixed. The error messages are more informative, and more aggressively prevent the user from risky or incorrect construction of the input file.

::DEVELOPER

MMB Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • VMD

:: DOWNLOAD

 MMB

:: MORE INFORMATION

Citation:

Samuel Coulbourn Flores, Russ B. Altman.
Structural insights into Pre-Translocation Ribosome Motions.
In Proceedings of Pacific Symposium on Biocomputing’2011. pp.205~216 (2011)

Samuel Flores and Russ Altman,
Turning limited experimental information into 3D models of RNA,
RNA 16(9):1769-78 (2010).

Omokage search – Shape Similarity Search of Macromolecules

Omokage search

:: DESCRIPTION

Omokage search” is a shape similarity search service for 3D structures of macromolecules. By comparing global shapes, and ignoring details, similar-shaped structures are searched.

::DEVELOPER

Omokage search team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.
Suzuki H, Kawabata T, Nakamura H.
Bioinformatics. 2015 Oct 27. pii: btv614.

CRDOCK – Dock Ligands in Macromolecules

CRDOCK

:: DESCRIPTION

CRDOCK is flexible tool to perform docking and virtual screening. The main goal of the program is the speed to be applicable in virtual screening.

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   CRDOCK

:: MORE INFORMATION

Citation

J Chem Inf Model. 2012 Aug 27;52(8):2300-9. doi: 10.1021/ci300194a. Epub 2012 Jul 19.
CRDOCK: an ultrafast multipurpose protein-ligand docking tool.
Cortés Cabrera á1, Klett J, Dos Santos HG, Perona A, Gil-Redondo R, Francis SM, Priego EM, Gago F, Morreale A.

VisProt3DS 3.03 – Stereoscopic Visual Analyzer of Biological Macromolecules

VisProt3DS 3.03

:: DESCRIPTION

VisProt3DS is a stereoscopic visual analyzer of biological macromolecules. Using VisProt3DS , you can look at Proteins and DNA (in PDB format) by the simplest and the cheapest stereo technology – Anaglyph stereo. VisProt3DS Anaglyph stereo mode can work on any usual computer (under the Windows) with color display, even on the NetBook with the weak built-in video card.

::DEVELOPER

VisProt3DS team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

VisProt3DS

:: MORE INFORMATION

Adepth – Measures of Atomic Depths in Macromolecules

Adepth

:: DESCRIPTION

Adepth computes the atom depths in proteins which is derived from trilinear interpolation of the signed distance function (SDF) at the nearest grid points surrounding the atom.

::DEVELOPER

BIODEV

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Adepth: new representation and its implications for atomic depths of macromolecules
Shu-wen W. Chen; Jean-Luc Pellequer
Nucleic Acids Research 2013

CryoBayes beta – Bayesian method for Inferring 3D structure of Macromolecules

CryoBayes beta

:: DESCRIPTION

CryoBayes is a Bayesian method for inferring 3D structure of macromolecules imaged by Electron Cryo-Microscopy experiments. We encourage experimental Structural Biologists to download and try our code. We hope that our technique will be useful as a method of automatically generating intial models given only class average images.

::DEVELOPER

Lilien Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

  CryoBayes

:: MORE INFORMATION

Citation:

Jaitly, N., Brubaker, M.A., Rubinstein, J.L. and Lilien, R.H.
A Bayesian Method for 3-D Macromolecular Structure Inference using Class Average Images from Single Particle Electron Microscopy,
Bioinformatics, 26(19):2406-15 (2010).

ProteinShader beta 0.9.4 – Illustrative Rendering of Macromolecules

ProteinShader beta 0.9.4

:: DESCRIPTION

ProteinShader is a new tool for macromolecular visualization, uses information from Protein Data Bank files to produce illustrative renderings of proteins that approximate what an artist might create by hand using pen and ink. A combination of Hermite and spherical linear interpolation is used to draw smooth, gradually rotating three-dimensional tubes and ribbons with a repeating pattern of texture coordinates, which allows the application of texture mapping, real-time halftoning, and smooth edge lines.

::DEVELOPER

Joe Weber, joe.weber AT alumni.duke.edu

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

ProteinShader

:: MORE INFORMATION

Citation

Joseph R Weber
ProteinShader: illustrative rendering of macromolecules
BMC Structural Biology 2009, 9:19

Protein Explorer 2.80 – Visualize 3D Structures of Macromolecules

Protein Explorer 2.80

:: DESCRIPTION

Protein Explorer is free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. It is arguably the easiest-to-use software of its kind.

::DEVELOPER

Eric Martz , the University of Massachusetts

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac

:: DOWNLOAD

Protein Explorer

:: MORE INFORMATION

Citation

Martz E.
Protein Explorer: easy yet powerful macromolecular visualization.
Trends Biochem Sci. 2002 Feb;27(2):107-9.