NMSim – Modeling Macromolecular Conformational Transitions

NMSim

:: DESCRIPTION

NMSim is a normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins.

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W310-6. doi: 10.1093/nar/gks478. Epub 2012 Jun 4.
NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.
Krüger DM1, Ahmed A, Gohlke H.

ccp4 6.5 – Macromolecular X-Ray Crystallography

ccp4 6.5

:: DESCRIPTION

ccp4 (Collaborative Computational Project No. 4) exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. CCP4 aims to develop and support the development of cutting edge approaches to experimental determination and analysis of protein structure, and integrate these approaches into the suite. CCP4 is a community based resource that supports the widest possible researcher community, embracing academic, not for profit, and for profit research. CCP4 aims to play a key role in the education and training of scientists in experimental structural biology. It encourages the wide dissemination of new ideas, techniques and practice.

:: DEVELOPER

ccp4 Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ccp4

:: MORE INFORMATION

Citation:

M. D. Winn et al. Acta. Cryst. D67 , 235-242 (2011)
Overview of the CCP4 suite and current developments
Acta Crystallographica Section D, Biological Crystallography,Volume 67, Part 4

MolSurfer 1.2 – a Macromolecular Interface Navigator

MolSurfer 1.2

:: DESCRIPTION

MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures.

:: DEVELOPER

Rebecca C. Wade

:: SCREENSHOTS

MolSurfer

:: REQUIREMENTS

  •  Linux /Windows/ MacOsX
  • Java

:: DOWNLOAD

 MolSurfer

:: MORE INFORMATION

Citation

Gabdoulline,R.R., Wade,R.C. and Walter,D.
MolSurfer: a macromolecular interface navigator
Nucl.Acid.Res. (2003) 31, 3349-3351.

LSim 1.0.0 – Superposes Macromolecular Electron Densities and Computes Structural Similarity Score

LSim 1.0.0

:: DESCRIPTION

LSim superposes macromolecular electron densities and computes a structural similarity score. LSim computations scale linearly with the size of the molecules being compared.

::DEVELOPER

Pere Constans

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LSim

:: MORE INFORMATION

Citation

Constans, P.
Linear Scaling Approaches to Quantum Macromolecular Similarity: Evaluating the Similarity Function.
J. Comput. Chem. 23, 1305-1313, 2002

PDBlib 2.2 – C++ Macromolecular Class Library

PDBlib 2.2

:: DESCRIPTION

PDBlib is an extensible object oriented class library, written in C++ for representing the 3-dimensional structure of biological macromolecules. The library models the structural features of proteins,DNA,RNA and complexes thereof, at a level of detail on a par with which can be parsed from a Brookhaven Protein Data Bank (PDB) entry. However, the memory resident representation of the macromolecule is independant of the PDB entry, and can be obtained from other sources such as relational, and object-oriented databases.

::DEVELOPER

the Bourne Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • C++ Complier

:: DOWNLOAD

 PDBlib

:: MORE INFORMATION

Citation:

W.Chang, I.N.Shindyalov, C.Pu, & P.E.Bourne,
Design and Application of PDBlib, a C++ Macromolecular Class Library.
Comput Appl Biosci (1994) 10(6), 575-586.