Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

(2013) Amelie Stein et al.   PLoS One

Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz

(2013) Rhiju Das   PLoS One

Loop prediction for a GPCR homology model: Algorithms and results

(2013) Dahlia A. Goldfeld et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ab initiostructure prediction of the antibody hypervariable H3 loop

(2013) Kai Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A database of immunoglobulins with integrated tools: DIGIT

(2011) A. Chailyan et al.   NUCLEIC ACIDS RESEARCH

Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors

(2011) D. A. Goldfeld et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling large regions in proteins: Applications to loops, termini, and folding

(2011) Aashish N. Adhikari et al.   PROTEIN SCIENCE

Critical assessment of methods of protein structure prediction (CASP)-round IX

(2011) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Progress in super long loop prediction

(2011) Suwen Zhao et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling

(2011) Jianing Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Antibody modeling assessment

(2011) Juan C. Almagro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

(2010) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

A New Clustering of Antibody CDR Loop Conformations

(2010) Benjamin North et al.   JOURNAL OF MOLECULAR BIOLOGY

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

(2009) Daniel J Mandell et al.   NATURE METHODS

PIGS: automatic prediction of antibody structures

(2008) P. Marcatili et al.   BIOINFORMATICS

Structural classification of CDR-H3 revisited: A lesson in antibody modeling

(2008) Daisuke Kuroda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Toward high-resolution homology modeling of antibody Fvregions and application to antibody-antigen docking

(2008) Arvind Sivasubramanian et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS