Secondary Structure and Conformational Stability of the Antigen Residues Making Contact with Antibodies

Mobility and disorder in antibody and antigen binding sites do not prevent immunochemical recognition

(2021) Vladimir N. Uversky et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Epitopes of Protein Binders Are Related to the Structural Flexibility of a Target Protein Surface

(2021) Dong-Gun Kim et al.   Journal of Chemical Information and Modeling

Analysis of Binding Modes of Antigen–Antibody Complexes by Molecular Mechanics Calculation

(2021) Liang Qu et al.   Journal of Chemical Information and Modeling

Assessing the Potency of β-Lactamase Inhibitors with Diverse Inactivation Mechanisms against the PenA1 Carbapenemase from Burkholderia multivorans

(2021) Michiyoshi Nukaga et al.   ACS Infectious Diseases

A human neutralizing antibody targets the receptor binding site of SARS-CoV-2

(2020) Rui Shi et al.   NATURE

Human neutralizing antibodies elicited by SARS-CoV-2 infection

(2020) Bin Ju et al.   NATURE

Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody

(2020) Dora Pinto et al.   NATURE

A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2

(2020) Yan Wu et al.   SCIENCE

Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies

(2020) Christopher O. Barnes et al.   CELL

Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike

(2020) Jiandong Huo et al.   Cell Host & Microbe

Structural basis of a shared antibody response to SARS-CoV-2

(2020) Meng Yuan et al.   SCIENCE

Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy

(2020) Shuo Du et al.   CELL

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

(2020) Christopher O. Barnes et al.   NATURE

An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain

(2020) Nicholas C. Wu et al.   Cell Reports

B-cell epitopes: Discontinuity and conformational analysis

(2019) Saba Ferdous et al.   MOLECULAR IMMUNOLOGY

Simulation Time Required for Diminishing the Initial Conformational Deviations among Protein Crystal Structures

(2018) Fei Qi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Development of a fluvoxamine detection system using a Quenchbody, a novel fluorescent biosensor

(2018) Ako Sasao et al.   Drug Testing and Analysis

MAbTope: A Method for Improved Epitope Mapping

(2018) Thomas Bourquard et al.   JOURNAL OF IMMUNOLOGY

Affinity Improvement of a Cancer-Targeted Antibody through Alanine-Induced Adjustment of Antigen-Antibody Interface

(2018) Takefumi Yamashita et al.   STRUCTURE

Cytosolic antibody delivery by lipid-sensitive endosomolytic peptide

(2017) Misao Akishiba et al.   Nature Chemistry

Computationally-driven identification of antibody epitopes

(2017) Casey K Hua et al.   eLife

Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit

(2016) Satoshi Fudo et al.   BIOCHEMISTRY

Roles of the respective loops at complementarity determining region on the antigen-antibody recognition

(2016) Tomonori Osajima et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface

(2016) John Wojcik et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proteome- pI : proteome isoelectric point database

(2016) Lukasz P. Kozlowski   NUCLEIC ACIDS RESEARCH

Classification epitopes in groups based on their protein family

(2015) Edgar Kozlova et al.   BMC BIOINFORMATICS

Antibody promiscuity: Understanding the paradigm shift in antigen recognition

(2015) Harmeet Kaur et al.   IUBMB LIFE

Thermodynamics of antibody–antigen interaction revealed by mutation analysis of antibody variable regions

(2015) Hiroki Akiba et al.   JOURNAL OF BIOCHEMISTRY

Deep Sequencing-guided Design of a High Affinity Dual Specificity Antibody to Target Two Angiogenic Factors in Neovascular Age-related Macular Degeneration

(2015) Patrick Koenig et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Rational design of viscosity reducing mutants of a monoclonal antibody: Hydrophobicversuselectrostatic inter-molecular interactions

(2015) Pilarin Nichols et al.   mAbs

AB-Bind: Antibody binding mutational database for computational affinity predictions

(2015) Sarah Sirin et al.   PROTEIN SCIENCE

Proteochemometric Modeling of the Antigen-Antibody Interaction: New Fingerprints for Antigen, Antibody and Epitope-Paratope Interaction

(2015) Tianyi Qiu et al.   PLoS One

Automated Identification of Complementarity Determining Regions (CDRs) Reveals Peculiar Characteristics of CDRs and B Cell Epitopes

(2014) Y. Ofran et al.   JOURNAL OF IMMUNOLOGY

Restricted Diversity of Antigen Binding Residues of Antibodies Revealed by Computational Alanine Scanning of 227 Antibody–Antigen Complexes

(2014) Gautier Robin et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational and statistical study on the molecular interaction between antigen and antibody

(2014) Tomonori Osajima et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition

(2014) Marc H. V. Van Regenmortel   JOURNAL OF MOLECULAR RECOGNITION

A series of PDB-related databanks for everyday needs

(2014) Wouter G. Touw et al.   NUCLEIC ACIDS RESEARCH

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

π–π Interactions in Structural Stability: Role in RNA Binding Proteins

(2013) V. Sivasakthi et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

TheHER2CISH pharmDx™Kit in the assessment of breast cancer patients for anti-HER2 treatment

(2013) Niels T Foged et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Energetic and Dynamic Aspects of the Affinity Maturation Process: Characterizing Improved Variants from the Bevacizumab Antibody with Molecular Simulations

(2013) Dario Corrada et al.   Journal of Chemical Information and Modeling

Binding and Aggregation Mechanism of Amyloid β-Peptides onto the GM1 Ganglioside-Containing Lipid Membrane

(2013) Tyuji Hoshino et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational B-Cell Epitope Prediction on Antigen Protein Structures: A Review of Current Algorithms and Comparison with Common Binding Site Prediction Methods

(2013) Bo Yao et al.   PLoS One

An analysis of B-cell epitope discontinuity

(2012) Ganesh N. Sivalingam et al.   MOLECULAR IMMUNOLOGY

Structural analysis of B-cell epitopes in antibody:protein complexes

(2012) Jens Vindahl Kringelum et al.   MOLECULAR IMMUNOLOGY

Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites

(2012) Gregory A. Ross et al.   PLoS One

Use of amino acid composition to predict epitope residues of individual antibodies

(2010) Shinji Soga et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Mining for the antibody-antigen interacting associations that predict the B cell epitopes

(2010) Liang Zhao et al.   BMC STRUCTURAL BIOLOGY

Technological progresses in monoclonal antibody production systems

(2009) Maria Elisa Rodrigues et al.   BIOTECHNOLOGY PROGRESS

Structural and Energetic Analysis on the Complexes of Clinically Isolated Subtype C HIV-1 Proteases and Approved Inhibitors by Molecular Dynamics Simulation

(2009) Shou Matsuyama et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational characterization of B-cell epitopes

(2007) Nimrod D. Rubinstein et al.   MOLECULAR IMMUNOLOGY