IMPACT | AGBNP | BEDAM | ASyncRE | UWHAM
Schrödinger Inc. Many of Schrödinger's products for structure-based drug discovery (Glide, Liaison, QSite, SiteMap, ProPrep, PrimeX) are based on the IMPACT molecular mechanics engine. I have contributed to some of these products as well as to the integration of IMPACT with the Maestro GUI. Recent academic development has been mainly centered on implicit solvent modeling (AGBNP, below), on replica exchange advanced conformational sampling (see for example ASyncRE, below), and protein-ligand binding free energy modeling (BEDAM).
Quick intro about the AGBNP API:
agbnp3_new(): creates a new AGBNP3 instance, needs things like charges, radii, etc.
agbnp3_agb_energy(): returns GB energies and derivatives + vdW energies and derivatives
The README file should give an idea of the work involved in plugging the AGBNP3 library into the molecular simulation code of your choice.
The workflow It takes as input .mae files of receptor and ligand plus a definition of the binding site region. Analysis of the results produce, among other things, the estimated values of the binding free energy. See the documentation and example provided.
Thanks to a generous grant from the NSF, BEDAM is being implemented also in the popular OpenMM package. An alpha release is expected in September 2015.
To install UWHAM enter:
within a R session. Documentation and examples are available within R by entering
> library("UWHAM") > help(uwham)
or in pdf format from
Variance estimation is based on the Fisher or Sandwich formulas, or, for correlated data, by block bootstrap. Processes corresponding to multiple independent simulations, serial tempering or serial Hamiltonian hopping simulations, and parallel replica exchange simulations of both the synchronous and asynchronous varieties are supported.
The UWHAM package is particularly robust in terms of scalability; we have been able to process within minutes large 2D replica exchange datasets with ~300,000 snapshots from ~200 thermodynamic states. Feedback, comments, and bug reports