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
   

more articles
Upcoming Workshops
Jan 22 2019 | PHILADELPHIA Area
Ligand-Based Drug Design and SAR Analysis
Advanced Structure-Based Drug Design

Feb 06 2019 | BASEL, Switzerland
Structure-Based Drug Design and Ligand Modification
Ligand-Based Drug Design and SAR Analysis

Feb 07 2019 | BASEL, Switzerland
Biologics: Protein Alignments, Modeling and Docking
Antibody Modeling and Protein Engineering in MOE

Feb 27 2019 | BOSTON Area
Structure-Based Drug Design and Ligand Modification
Small Molecule Virtual Screening

Feb 28 2019 | BOSTON Area
Antibody Modeling and Protein Engineering in MOE
Biologics: Protein Alignments, Modeling and Docking

Mar 06 2019 | SAN DIEGO
Antibody Modeling and Protein Engineering in MOE
Biologics: Protein Alignments, Modeling and Docking

more workshops in North America more workshops in Europe
Upcoming Webinars
more webinars
Upcoming Events
Dec 09 - 13, 2018 | San Diego, CA
Antibody Engineering and Therapeutics Conference

Mar 24 - 26, 2019 | Cambridge, UK
7th RSC-BMCS Fragment-based Drug Discovery meeting

Mar 31 - Apr 04, 2019 | Orlando, FL
ACS Spring Meeting & Exposition

Apr 08 - 12, 2019 | San Diego, CA
Drug Discovery Chemistry

Apr 08 - 12, 2019 | Boston, MA
PEGS

more events
SVL Exchange
The Scientific Vector Language (SVL) code exchange is a site for the MOE™ user community.
SVL Exchange
News
June 11, 2018
Chemical Computing Group Announces The Winners of the COMP CCG Research Excellence Awards for the Fall 2018 ACS National Meeting

June 11, 2018
Chemical Computing Group Announces The Winners of the MEDI CCG Research Excellence Awards for the Fall 2018 ACS National Meeting

April 04, 2018
Chemical Computing Group Releases PSILO 2017.12

February 08, 2018
Chemical Computing Group Releases MOE 2018.01

January 11, 2018
Chemical Computing Group Announces The Winners of the COMP CCG Research Excellence Awards for the Spring 2018 ACS National Meeting

January 11, 2018
Chemical Computing Group Announces The Winners of the MEDI CCG Research Excellence Awards for the Spring 2018 ACS National Meeting

more news
  Site Map | Legal Notice