Category: 3D molecular model

Hollow 1.3 – Illustration software for Proteins

Hollow 1.3

:: DESCRIPTION

HOLLOW facilitates the production of surface images of proteins. Hollow generates fake atoms that identifies voids, pockets, channels and depressions in a protein structure specified in the PDB format.

::DEVELOPER

Hollow team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Python

:: DOWNLOAD

Hollow

:: MORE INFORMATION

Bosco K. Ho and Franz Gruswitz
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures (2008)
BMC Structural Biology 8:49

CafeMol 3.2.1 – Biomolecular Modeling and Simulation Software

CafeMol 3.2.1

:: DESCRIPTION

CafeMol is a general-purpose coarse-grained(CG) biomolecular modeling and simulation software.It can simulate proteins,nucleic acids,lipids and their mixture with various CG models.

::DEVELOPER

Takada Lab ，Kyoto University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Fortran90/95
  •  C compiler

:: DOWNLOAD

 CafeMol

:: MORE INFORMATION

Citation

Hiroo Kenzaki, Nobuyasu Koga, Naoto Hori, Ryo Kanada, Wenfei Li, Kei-ichi Okazaki, Xin-Qiu Yao, and Shoji Takada ,
CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work,
Journal of Chemical Theory and Computation , 7: 1979-1989, 2011

QuickLookPDB – QuickLook plugin for Displaying PDB Files

QuickLookPDB

:: DESCRIPTION

QuickLookPDB is the QuickLook plugin for displaying PDB files and provides two visualisation options. plugin can use pymol to quickly render thumbnail images, while the heart of the plugin lies with the integration of a HTML-5 PDB viewer, Jolecule.

::DEVELOPER

Ben Porebski

:: SCREENSHOTS

QuickLookPDB

:: REQUIREMENTS

  • Mac OsX

:: DOWNLOAD

 QuickLookPDB

:: MORE INFORMATION

RedMD 2.3 – Perform Molecular Dynamics Simulations for Coarse-grained Models

RedMD 2.3

:: DESCRIPTION

RedMD (Reduced Molecular Dynamics) is a an open source software to perform molecular dynamics simulations for coarse-grained models of proteins, nucleic acids and their complexes. Simulations can be carried out in the microcanonical ensemble, with Berendsen and Langevin thermostats, as well as with Brownian dynamics.

::DEVELOPER

Biomolecular Machines Laboratory 

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RedMD

:: MORE INFORMATION

Citation

Adam Gorecki, Marcin Szypowski, Maciej Dlugosz, Joanna Trylska,
RedMD – reduced molecular dynamics package,
J. Comput. Chem., 30:2364-2373, 2009

BD_BOX 1.2 – Brownian Dynamics Simulation

BD_BOX 1.2

:: DESCRIPTION

BD_BOX is an open source, scalable Brownian dynamics package for UNIX/LINUX platforms. BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds.

::DEVELOPER

Biomolecular Machines Laboratory 

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BD_BOX

:: MORE INFORMATION

Citation

Maciej Długosz, Paweł Zieliński Joanna Trylska,
Brownian dynamics simulations on CPU and GPU with BD_BOX,
J. Comput. Chem., 32:2734–2744, 2011

Surface Diver – Comparing, and Classifying Proteins according to their Physicochemical Properties

Surface Diver

:: DESCRIPTION

Surface Diver allows describing, comparing, and classifying proteins according to their physicochemical properties without the need of prior 3D structural alignment.

::DEVELOPER

Biomolecular Machines Laboratory 

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Surface Diver

:: MORE INFORMATION

Citation

Maciej Dlugosz, Joanna Trylska
Electrostatic similarity of proteins: Application of 3D spherical harmonic decomposition,
J. Chem. Phys., 129:015103, 2008

ORTEP-III 1.03 /for Windows 2021.3 – Crystal Structure Illustration

ORTEP-III 1.03 /for Windows2021.3

:: DESCRIPTION

ORTEP-III is Oak Ridge Thermal Ellipsoid Plot Program for crystal structure illustrations.Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites. The program also produces stereoscopic pairs of illustrations which aid in the visualization of complex arrangements of atoms and their correlated thermal motion patterns.

Ortep-3 for Windows developed by Dr. Louis Farrugia is a MS-Windows version of the current release of ORTEP-III

::DEVELOPER

Michael N. Burnett and Carroll K. Johnson

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux /
  • POV-Ray

:: DOWNLOAD

ORTEP-III ; Ortep-3 for Windows

:: MORE INFORMATION

Citation:

Michael N. Burnett and Carroll K. Johnson,
ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations,
Oak Ridge National Laboratory Report ORNL-6895, 1996.

WinGX and ORTEP for Windows: an update
L. J. Farrugia,
J. Appl. Cryst (2012), 45, 849-854.

SelfAT-Fold – Protein Fold Recognition

SelfAT-Fold

:: DESCRIPTION

selfAT-fold: protein fold recognition based on residue-based and motif-based self-attention networks

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SelfAT-Fold

:: MORE INFORMATION

Citation

Pang Y, Liu B.
SelfAT-Fold: protein fold recognition based on residue-based and motif-based self-attention networks.
IEEE/ACM Trans Comput Biol Bioinform. 2020 Oct 22;PP. doi: 10.1109/TCBB.2020.3031888. Epub ahead of print. PMID: 33090951.