3D Antibody Modeling 

Almagro JC, Beavers MP, Hernandez-Guzman F, Maier J, Shaulsky J, Butenhof K, Labute P, Thorsteinson N, Kelly K, Teplyakov A, Luo J, Sweet R, Gilliland GL. Antibody modeling assessment. Proteins. 2011 Nov;79(11):3050-66.

Almagro JC, Teplyakov A, Luo J, Sweet RW, Kodangattil S, Hernandez-Guzman F, Gilliland GL.Second Antibody Modeling Assessment (AMA-II). Proteins. 2014 Mar 26. doi: 10.1002/prot.24567. [Epub ahead of print]

Teplyakov A, Luo J, Obmolova G, Malia TJ, Sweet R, Stanfield RL, Kodangattil S, Almagro JC, Gilliland GL. Antibody modeling assessment II: Structures and models. Proteins. 2014 Mar 14. doi: 10.1002/prot.24554. [Epub ahead of print]

Weitzner BD1, Kuroda D, Marze N, Xu J, Gray JJ. Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization. Proteins. 2014 Feb 12. doi: 10.1002/prot.24534. [Epub ahead of print]

Zhu K, Day T, Warshaviak D, Murrett C, Friesner R, Pearlman D. Antibody Structure Determination Using a Combination of Homology Modeling, Energy-Based Refinement and Loop Prediction. Proteins. 2014 Mar 12. doi: 10.1002/prot.24551. [Epub ahead of print]

Zhu K, Day T, Warshaviak D, Murrett C, Friesner R, Pearlman D. 
Antibody Structure Determination Using a Combination of Homology Modeling, Energy-Based Refinement and Loop Prediction\\

 

JK Maier, P Labute. Assessment of fully automated antibody homology modeling protocols in molecular operating environment. Proteins. 2014 Apr 9.[Epub ahead of print]


Shirai H, Ikeda K, Yamashita K, Tsuchiya Y, Sarmiento J, Liang S, Morokata T, Mizuguchi K, Higo J, Standley DM, Nakamura H. High?resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations. Proteins. 2014 Apr 22.[Epub ahead of print]

Berrondo M, Kaufmann S, Berrondo M. Automated aufbau of antibody structures from given sequences using macromoltek's SmrtMolAntibody. Proteins. 2014 Apr 29. [Epub ahead of print]

Fasnacht M1, Butenhof K, Goupil-Lamy A, Hernandez-Guzman F, Huang H, Yan L. Automated antibody structure prediction using Accelrys tools: Results and best practices. Proteins. 2014 May 16. [Epub ahead of print]