Robustification of RosettaAntibody and Rosetta SnugDock

KORP: Knowledge-based 6D potential for fast protein and loop modeling

(2019) José Ramón López-Blanco et al.   BIOINFORMATICS

Non-H3 CDR template selection in antibody modeling through machine learning

(2019) Xiyao Long et al.   PeerJ

Modeling Antibody-Antigen Complexes by Information-Driven Docking

(2019) Francesco Ambrosetti et al.   STRUCTURE

Novel sampling strategies and a coarse‐grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37–45

(2019) Shourya S. Roy Burman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Efficient flexible backbone protein–protein docking for challenging targets

(2018) Nicholas A Marze et al.   BIOINFORMATICS

Structurally Mapping Antibody Repertoires

(2018) Konrad Krawczyk et al.   Frontiers in Immunology

SCALOP: sequence-based antibody canonical loop structure annotation

(2018) Wing Ki Wong et al.   BIOINFORMATICS

abYsis: Integrated Antibody Sequence and Structure—Management, Analysis, and Prediction

(2017) Mark B. Swindells et al.   JOURNAL OF MOLECULAR BIOLOGY

Modeling and docking of antibody structures with Rosetta

(2017) Brian D Weitzner et al.   Nature Protocols

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

PIGSPro: prediction of immunoGlobulin structures v2

(2017) Rosalba Lepore et al.   NUCLEIC ACIDS RESEARCH

The H3 loop of antibodies shows unique structural characteristics

(2017) Cristian Regep et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computationally-driven identification of antibody epitopes

(2017) Casey K Hua et al.   eLife

FRODOCK 2.0: fast protein–protein docking server

(2016) Erney Ramírez-Aportela et al.   BIOINFORMATICS

Structural Analysis of Single Domain Antibodies Bound to a Second Neutralizing Hot Spot on Ricin Toxin's Enzymatic Subunit

(2016) Michael J. Rudolph et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ABodyBuilder: Automated antibody structure prediction with data–driven accuracy estimation

(2016) Jinwoo Leem et al.   mAbs

Improved prediction of antibody VL–VHorientation

(2016) Nicholas A. Marze et al.   PROTEIN ENGINEERING DESIGN & SELECTION

The promise and challenge of high-throughput sequencing of the antibody repertoire

(2014) George Georgiou et al.   NATURE BIOTECHNOLOGY

Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization

(2014) Brian D. Weitzner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Second antibody modeling assessment (AMA-II)

(2014) Juan C. Almagro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SAbDab: the structural antibody database

(2013) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

(2013) Amelie Stein et al.   PLoS One

Application of asymmetric statistical potentials to antibody-protein docking

(2012) R. Brenke et al.   BIOINFORMATICS

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

A New Clustering of Antibody CDR Loop Conformations

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

An integrated suite of fast docking algorithms

(2010) Efrat Mashiach et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

(2010) Aroop Sircar et al.   PLoS Computational Biology

Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains

(2008) K.R. Abhinandan et al.   MOLECULAR IMMUNOLOGY