|MOE: Molecular Operating Environment|
|Major New Features in MOE 2018.01|
|Major New Features in PSILO 2016.10|
|Assessment of fully automated antibody homology modeling protocols in molecular operating environment|
Johannes K. X. Maier and Paul Labute
We present a method for automatic modeling of the FV region of an immunoglobulin based upon the use of a precompiled antibody x-ray structure database, which serves as a source of framework and hypervariable region structural templates that are grafted together. We applied this method (on common desktop hardware) to the Second Antibody Modeling Assessment (AMA-II) target structures as well as an experimental specialized CDR-H3 loop modeling method. The results of the computational structure predictions will be presented and discussed.
Proteins, 2014 82: 1599–1610. doi:10.1002/prot.24576
|A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies|
Jean-François Truchon, B. Montgomery Pettitt, and Paul Labute
We show that an Ng bridge function modified version of the three-dimensional reference interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict the hydration free energy (HFE) of a set of 504 organic molecules.
J. Chem. Theory Comput., 2014 (Article ASAP), doi:10.1021/ct4009359
|Identifying Structural Domains of Proteins Using Clustering|
Howard J Feldman
This study presents a novel clustering-based approach to domain identification, which works equally well on individual chains or entire complexes. The method is competitive with others, achieving 70% agreement with SCOP on a large non-redundant data set, and 80% on a set more heavily weighted in multi-domain proteins on which both SCOP and CATH agree.
BMC Bioinformatics, 2012, 13:286 doi:10.1186/1471-2105-13-286
|Variability in Docking Success Rates Due to Dataset Preparation|
C. R. Corbeil, C. I. Williams and P. Labute
The MOE software with the newly developed GBVI/WSA dG scoring function is used throughout the study. For 80 % of the Astex targets, the MOE docker produces a top-scoring pose within 2 Å of the X-ray structure. For 91 % of the targets a pose within 2 Å of the X-ray structure is produced in the top 30 poses.
J Comput Aided Mol Des, 2012, 26 (6), pp 775-786