Shape complementarity and hydrogen bond preferences in protein–protein interfaces: implications for antibody modeling and protein–protein docking

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

(2015) Thom Vreven et al.   JOURNAL OF MOLECULAR BIOLOGY

The Origin of CDR H3 Structural Diversity

(2015) Brian D. Weitzner et al.   STRUCTURE

Origins of specificity and affinity in antibody–protein interactions

(2014) Hung-Pin Peng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cation-π, amino-π, π-π, and H-bond interactions stabilize antigen-antibody interfaces

(2014) Georgios A. Dalkas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SAbDab: the structural antibody database

(2013) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

Local Network Patterns in Protein-Protein Interfaces

(2013) Qiang Luo et al.   PLoS One

ABangle: characterising the VH-VL orientation in antibodies

(2013) J. Dunbar et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Antigen–antibody interface properties: Composition, residue interactions, and features of 53 non-redundant structures

(2012) Thiruvarangan Ramaraj et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds

(2012) P. Benjamin Stranges et al.   PROTEIN SCIENCE

The association of heavy and light chain variable domains in antibodies: implications for antigen specificity

(2011) Anna Chailyan et al.   FEBS Journal

Antibody modeling assessment

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

Adhesive water networks facilitate binding of protein interfaces

(2011) Mazen Ahmad et al.   Nature Communications

Geometric Similarities of Protein–Protein Interfaces at Atomic Resolution Are Only Observed within Homologous Families: An Exhaustive Structural Classification Study

(2010) Akira R. Kinjo et al.   JOURNAL OF MOLECULAR BIOLOGY

Analysis and prediction of VH/VL packing in antibodies

(2010) K. R. Abhinandan et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: Implications for the protein docking problem

(2010) Richard M. Jackson   PROTEIN SCIENCE

Energy-Based Analysis and Prediction of the Orientation between Light- and Heavy-Chain Antibody Variable Domains

(2009) Arjun Narayanan et al.   JOURNAL OF MOLECULAR BIOLOGY

Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?

(2008) Ozlem Keskin et al.   CHEMICAL REVIEWS

Targeting and tinkering with interaction networks

(2008) Robert B Russell et al.   Nature Chemical Biology

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

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

Protein–protein interaction and quaternary structure

(2008) Joël Janin et al.   QUARTERLY REVIEWS OF BIOPHYSICS