HADDOCK consists of a collection of python and CNS scripts and some other additional programs and scripts (csh, awk, perl, c++). Needed:
- CNS (https://cns-online.org): MANDATORY to run HADDOCK, TO BE OBTAINED AND INSTALL SEPARATELY
Also recommended are:
Naccess is a stand alone program that calculates the accessible area
of a molecule from a PDB format file. It can calculate the atomic and
residue accessibilities for both proteins and nucleic acids, and is
available for free of charge for researchers at academic and non
profit-making institutions. We make use of NACCESS in HADDOCK to filter
active and passive residues based on their solvent accessible area (see
section AIR restraints).
- ProFit: ProFit is
designed to be the ultimate protein least squares fitting program. Some of
the provided analysis tools in HADDOCK make use of Profit. Profit can
be obtained free of charge for academics at https://www.bioinf.org.uk/software
PALES is a software for analysis of residual dipolar couplings. Pales provides
features for analysis of experimental dipolar couplings and dipolar coupling tensors,
such as best-fitting a dipolar coupling tensor to its corresponding 3D structure.
Pales can thus be used to derive the tensor components (Dxx, Dyy, Dzz or Da and R)
needed for the use of dipolar couplings as restraints for docking.
- Module: Modules is
another useful software for analysis of residual dipolar couplings with a nice
graphical interface. Modules allows the determination of alignment tensor
parameters for individual or multiple domains in macromolecules from residual
dipolar couplings and facilitates their manipulation to construct low-resolution
models of macromolecular structure.
- Tensor: Tensor is
another useful software for analysis of diffusion anisotropy data (NMR relaxation) with a nice
graphical interface. Tensor2 allows the determination of alignment tensor
parameters for individual or multiple domains in macromolecules from diffusion anisotropy data
and facilitates their manipulation to construct low-resolution models of macromolecular structure.
- 3DNA: 3DNA is a versatile package for
the analysis, rebuilding, and visualization of three-dimensional nucleic acid structures, based on a standard
reference frame (Olson et al., J. Mol. Biol. 313, 229-237, 2001). It is the software we
are using to generate libraries of pre-bent DNA conformations for protein-DNA docking in
our 3D-DART web server.
Here are a few links to other useful software:
The ultimate structure validation software suite... As a web portal. CING stands for
Common Interface for NMR structure Generation and is known for structure and NMR data validation.
Another nice structure validation server which integrates analyses from several widely-used structure quality evaluation tools,
including RPF, PROCHECK, MolProbity, Verify3D, Prosa II, the PDB validation software, and various structure-validation tools.
LIGPLOT is a program for automatically plotting protein-ligand interactions or protein-protein
interactions (use for that dimplot). It automatically generates schematic diagrams of protein-ligand
interactions for a given PDB file. The interactions shown are those mediated by hydrogen bonds and by
NUCPLOT is a program for automatically plotting protein-nucleic acid interactions.
NUCPLOT can generate schematic diagrams automatically - directly from the 3D coordinates of the
complex as found in a given PDB file. The program works for any single- or double-stranded protein-DNA,
DNA-ligand and protein-RNA complexes.
- WhatIF This is a program
for protein structure analysis, validation and repair. It is available as a
A very nice graphing tool for UNIX.
This molecular graphics program displays your PDB
structures on screen using X graphics and enables you to rotate, display
and color the structure in a number of ways. Very convenient for a Quick
look at a structure. We use it for example to display, select and color
active and passive residues for HADDOCK (see
section AIR restraints)
- Pymol This is a very nice visualization (and much more)
program for high-quality display of 3D molecular structures.
- Molscript This is a
script-driven program for high-quality display of molecular 3D structures
in both schematic and detailed representations. You can get an academic
license for free from Avatar.
Here are a few links to scoring-related software:
- MOLPROBITY: MOLPROBITY can be used to
assess the packing and hydrogen-bonding quality of an interface.
- CCHarPPI: CCharPPI integrates many binding affinity
and scoring functions into a single web server. It calculates up to 108 parameters, including models of electrostatics,
desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials
at various resolutions, docking potentials and composite scoring functions.
- FastContact: FastContact is a
free energy scoring tool for protein-protein complex structures based on electrostatic and desolvation energies.
- DComplex: DComplex uses the
DFIRE energy function for the prediction of binding affinities.
- FoldX: FoldX is a program for calculating the folding pathways of
proteins and for calculating the effect of a point mutation on the stability of a protein.
- PISA: PISA is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies, as well as searches on various assembly and PDB entry parameters.