Modeling Macromolecular Complexes: A Journey Across Scales - Modeling in Computational Biology and Biomedicine - page 37

are offered, with different tools and connexions with complementary informtion in
structural biology, biology, and bioinformatics.
The IMGT/3D-structure database
http://www.imgt.org/3Dstructure-DB
This database provides annotated versions of complexes from the immune system,
retrieved on a weekly basis from the PDB.
The Unified Data Resource for 3-Dimensional Electron Microscopys
http://emdatabank.org
The EMDataBank is the sister of the PDB, for cryo-electron microscopy models.
Protein-protein docking Benchmark
http://zlab.umassmed.edu/benchmark
The docking benchmark contains annotations regarding the three-dimensional
structures (X-ray and NMR) of protein-protein complexes together with the cor-
responding structures of the unbound components.
Protein-Protein Interaction Affinity Database
http://bmm.cancerresearchuk.org/ ∼ bmmadmin/Affinity/
This database provides crystal structures of protein complexes together with those
of the unbound partners, as well as experimentally measured binding affinities.
See also [ 39 ].
1.5.2 Software
1.5.2.1 Molecular Dynamics Simulation
Several programs are commonly used to simulate macromolecular dynamics at
atomic resolution in either implicit or explicit solvent. Among the most commonly
used are
Amber
http://ambermd.org
Amber consists of a molecular force field, together with a suite of programs allowing
users to perform molecular dynamics simulations.
Charmm
http://www.charmm.org
Chemistry at HARvard Macromolecular Mechanics is one of the oldest molecular
simulation packages.
NAMD
http://www.ks.uiuc.edu/Research/namd
Not (just) Another Molecular Dynamics program is a molecular dynamics code with
strong emphasis on parallel calculations, that in addition can be linked to the Visual
Molecular Dynamics visualization environment (see below).