Germline-Dependent Antibody Paratope States and Pairing Specific VH-VL Interface Dynamics

X-Entropy: A Parallelized Kernel Density Estimator with Automated Bandwidth Selection to Calculate Entropy

(2021) Johannes Kraml et al.   Journal of Chemical Information and Modeling

Mutation of Framework Residue H71 Results in Different Antibody Paratope States in Solution

(2021) Monica L. Fernández-Quintero et al.   Frontiers in Immunology

Antibody humanization—the Influence of the antibody framework on the CDR-H3 loop ensemble in solution

(2020) Monica L Fernández-Quintero et al.   PROTEIN ENGINEERING DESIGN & SELECTION

V H ‐V L interdomain dynamics observed by computer simulations and NMR

(2020) Monica L. Fernández‐Quintero et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

T-Cell Receptor Variable β Domains Rigidify During Affinity Maturation

(2020) Monica L. Fernández-Quintero et al.   Scientific Reports

Conformational changes in a Vernier zone region: Implications for antibody dual specificity

(2020) Merve Arslan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

T-Cell Receptor CDR3 Loop Conformations in Solution Shift the Relative Vα-Vβ Domain Distributions

(2020) Monica L. Fernández-Quintero et al.   Frontiers in Immunology

Local and Global Rigidification Upon Antibody Affinity Maturation

(2020) Monica L. Fernández-Quintero et al.   Frontiers in Molecular Biosciences

Polyreactive Broadly Neutralizing B cells Are Selected to Provide Defense against Pandemic Threat Influenza Viruses

(2020) Jenna J. Guthmiller et al.   IMMUNITY

Antibodies exhibit multiple paratope states influencing VH–VL domain orientations

(2020) Monica L. Fernández-Quintero et al.   Communications Biology

Conformational Ensembles of Antibodies Determine Their Hydrophobicity

(2020) Franz Waibl et al.   BIOPHYSICAL JOURNAL

Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments

(2020) Monica L. Fernández-Quintero et al.   Frontiers in Molecular Biosciences

Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties

(2019) Monica L. Fernández-Quintero et al.   Frontiers in Immunology

CDR-H3 loop ensemble in solution – conformational selection upon antibody binding

(2019) Monica L. Fernández-Quintero et al.   mAbs

Variational Approach for Learning Markov Processes from Time Series Data

(2019) Hao Wu et al.   JOURNAL OF NONLINEAR SCIENCE

Transitions of CDR-L3 Loop Canonical Cluster Conformations on the Micro-to-Millisecond Timescale

(2019) Monica L. Fernández-Quintero et al.   Frontiers in Immunology

Antibodies to watch in 2020

(2019) Hélène Kaplon et al.   mAbs

Metadynamics Enhanced Markov Modeling of Protein Dynamics

(2018) Mithun Biswas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural insights into humanization of anti-tissue factor antibody 10H10

(2018) Alexey Teplyakov et al.   mAbs

Antigen binding allosterically promotes Fc receptor recognition

(2018) Jun Zhao et al.   mAbs

Modeling and docking of antibody structures with Rosetta

(2017) Brian D Weitzner et al.   Nature Protocols

The H3 loop of antibodies shows unique structural characteristics

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

Antibody H3 Structure Prediction

(2017) C. Marks et al.   Computational and Structural Biotechnology Journal

Structural diversity in a human antibody germline library

(2016) Alexey Teplyakov et al.   mAbs

Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions

(2016) Catherine L. Townsend et al.   Frontiers in Immunology

ANARCI: antigen receptor numbering and receptor classification

(2015) James Dunbar et al.   BIOINFORMATICS

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

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

VH-VL orientation prediction for antibody humanization candidate selection: A case study

(2015) Alexander Bujotzek et al.   mAbs

Prediction of VH-VL domain orientation for antibody variable domain modeling

(2015) Alexander Bujotzek et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

PyIgClassify: a database of antibody CDR structural classifications

(2014) Jared Adolf-Bryfogle et al.   NUCLEIC ACIDS RESEARCH

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge

(2013) Jochen S. Hub et al.   Journal of Chemical Theory and Computation

Well-Tempered Metadynamics as a Tool for Characterizing Multi-Component, Crystalline Molecular Machines

(2013) Andrew J. Ilott et al.   JOURNAL OF PHYSICAL CHEMISTRY B

ABangle: characterising the VH-VL orientation in antibodies

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

Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification

(2013) Susanna Röblitz et al.   Advances in Data Analysis and Classification

Germline VH/VL pairing in antibodies

(2012) N. Jayaram et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for type I/II distinction of CD20 antibodies

(2011) G. Niederfellner et al.   BLOOD

A challenging system: Free energy prediction for factor Xa

(2011) Hannes G. Wallnoefer et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Structure and function of immunoglobulins

(2010) Harry W. Schroeder et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

A New Clustering of Antibody CDR Loop Conformations

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

The influence of the framework core residues on the biophysical properties of immunoglobulin heavy chain variable domains

(2009) Annemarie Honegger et al.   PROTEIN ENGINEERING DESIGN & SELECTION

IMGT(R), the international ImMunoGeneTics information system(R)

(2008) M.-P. Lefranc et al.   NUCLEIC ACIDS RESEARCH

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures

(2008) Paul Labute   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Interaction between the antigen and antibody is controlled by the constant domains: Normal mode dynamics of the HEL-HyHEL-10 complex

(2003) Masaaki Adachi et al.   PROTEIN SCIENCE