Assessment of fully automated antibody homology modeling protocols in molecular operating environment
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

Wiley Open Access
A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies
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

ACS AuthorChoice: Free Access
Identifying Structural Domains of Proteins Using Clustering
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

BioMed Central Open Access
Variability in Docking Success Rates Due to Dataset Preparation
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

Springer Open Access
Scaffold Replacement in MOE
Scaffold Replacement in MOE
S. Grimshaw

A new application for performing scaffold replacements, fragment linking, and R-group optimization is presented. The application is applied to the discovery of novel p38 MAP kinase inhibitors, using the structures of a screening hit and the mature BIRB-796 inhibitor as starting points.

Training a Scoring Function for the Alignment of Small Molecules
Training a Scoring Function for the Alignment of Small Molecules
S. L. Chan and P. Labute

A comprehensive data set of aligned ligands with highly similar binding pockets from the Protein Data Bank has been built. Based on this data set, a scoring function for recognizing good alignment poses for small molecules has been developed.
J Chem Inf Model, 2010, 50 (9), pp 1724-1735

ACS AuthorChoice: Free Access
Calibrative approaches to protein solubility modeling of a mutant series using physicochemical descriptors
Calibrative approaches to protein solubility modeling of a mutant series using physicochemical descriptors
W. F. Long and P. Labute

A set of physicochemical properties describing a protein of known structure is employed for a calibrative approach to protein solubility.
J Comput Aided Mol Des, 2010, 24 (11), pp 907-916

Springer Open Access
Pocket Similarity: Are α Carbons Enough?
Pocket Similarity: Are α Carbons Enough?
H. J. Feldman and P. Labute

A novel method for measuring protein pocket similarity was devised, using only the α carbon positions of the pocket residues.
J Chem Inf Model, 2010, 50 (8), pp 1466-1475

ACS AuthorChoice: Free Access
LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops
LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops
P. Labute

We present a method for conformational search of complex molecular systems such as macrocycles and protein loops.
J Chem Inf Model, 2010, 50 (5), pp 792-800

ACS AuthorChoice: Free Access
SD File Processing with MOE Pipeline Tools
SD File Processing with MOE Pipeline Tools
A. M. Clark and P. Labute

We present a series of SD command line tools for the preparation of small molecule databases including protonation and tautomer enumeration, filtering, sorting and descriptor calculations.

Ligand Scaffold Replacement using MOE Pharmacophore Tools
Ligand Scaffold Replacement using MOE Pharmacophore Tools
A. Deschênes and E. Sourial

We describe a scaffold replacement methodology based upon an extension of MOE's pharmacophore features. The special "Link" pharmacophore features can be used in conjunction with other features, SMARTS patterns and volume constraints.

Protonate 3D: Assignment of Macromolecular Protonation State and Geometry
Protonate 3D: Assignment of Macromolecular Protonation State and Geometry
P. Labute

Protonate 3D is an application which assigns protonation states and geometries (taking titration into account) to macromolecular structures using an algorithm that solves the Unary Quadratic Optimization problem.

Ligand Interaction Diagrams
Ligand Interaction Diagrams
A. M. Clark

2D active site diagrams showing the ligand, nearby residues and various types of interactions.

Active Site Visualization and Analysis
Active Site Visualization and Analysis
P. Labute

An Integrated Application in MOE for the Visualization and Analysis of Protein Active Sites with Molecular Surfaces, Contact Statistics and Electrostatic Maps.

2D Structure Depiction
2D Structure Depiction
A. M. Clark

Structure diagrams can be generated from molecular connection tables in MOE.

Molecular Orbitals in MOE
Molecular Orbitals in MOE
A. M. Clark

New functionality in MOE for plotting molecular orbitals generated from MOPAC wavefunctions.

Relational Database Access in MOE
Relational Database Access in MOE
S. Burlington

An overview of the JDBC model used in MOE for connecting to and manipulating relational databases.