Computationally, using the Molecular Dynamics tools, you can predict the conformational changes due to binding. You can predict the stability of the protein-protein binding in terms of the binding free energies and compare this with experimental results. You can do binding energy decomposition per residue and calculate the changes in the binding energy due to mutations of the residues, especially these that are in the binding site (typically, you can mutate a residue to alanine). You can calculate the entropic distributions to the binding.
The software that can perform molecular dynamics simulations include namd, charmm, gromacs, desmond, and others.
You can do simulations in different solvent environments, most typically water + salts (NaCl, KCl), which mimic biological environment, You can do simulations under different constraints, for example, fixed number of particles, temperature and volume or pressure to reproduce experimental conditions.
Computationally, using the Molecular Dynamics tools, you can predict the conformational changes due to binding. You can predict the stability of the protein-protein binding in terms of the binding free energies and compare this with experimental results. You can do binding energy decomposition per residue and calculate the changes in the binding energy due to mutations of the residues, especially these that are in the binding site (typically, you can mutate a residue to alanine). You can calculate the entropic distributions to the binding.
The software that can perform molecular dynamics simulations include namd, charmm, gromacs, desmond, and others.
You can do simulations in different solvent environments, most typically water + salts (NaCl, KCl), which mimic biological environment, You can do simulations under different constraints, for example, fixed number of particles, temperature and volume or pressure to reproduce experimental conditions.
Are you trying to:
1. Predict which proteins interact from a large set of sequences
2. Predict the structures of the protein complexes from a large set
3. Predict the strength of interaction for a small set of proteins
The methods are different for each.
Prediction of protein-protein interactions between human host and a pathogen and its application to three pathogenic bacteria
http://www.ncbi.nlm.nih.gov/pubmed/21310175
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