Journal Articles

Assessment of fully automated antibody homology modeling protocols in molecular operating environmentAssessment 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
Wiley Open Access
   

A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free EnergiesA 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
ACS AuthorChoice: Free Access
   

Identifying Structural Domains of Proteins Using ClusteringIdentifying 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
BioMed Central Open Access
   

Variability in Docking Success Rates Due to Dataset PreparationVariability 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
Springer Open Access
   

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