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

Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification

(2018) Jeliazko R. Jeliazkov et al.   Frontiers in Immunology

tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables

(2017) Mohammad M. Sultan et al.   Journal of Chemical Theory and Computation

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

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

(2016) Daisuke Kuroda et al.   BIOINFORMATICS

Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2

(2016) Christian R. Schwantes et al.   BIOPHYSICAL JOURNAL

Hierarchical Time-Lagged Independent Component Analysis: Computing Slow Modes and Reaction Coordinates for Large Molecular Systems

(2016) Guillermo Pérez-Hernández et al.   Journal of Chemical Theory and Computation

Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD

(2016) Anna S. Kamenik et al.   Journal of Chemical Theory and Computation

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

(2016) Brandon J. DeKosky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Somatic Hypermutation-Induced Changes in the Structure and Dynamics of HIV-1 Broadly Neutralizing Antibodies

(2016) Thaddeus M. Davenport et al.   STRUCTURE

Adaptive Mutations Alter Antibody Structure and Dynamics during Affinity Maturation

(2015) Ramkrishna Adhikary et al.   BIOCHEMISTRY

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

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

Polyreactive Antibodies: Function and Quantification

(2015) Sreenivasulu Gunti et al.   JOURNAL OF INFECTIOUS DISEASES

The Origin of CDR H3 Structural Diversity

(2015) Brian D. Weitzner et al.   STRUCTURE

Markov state models of biomolecular conformational dynamics

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

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

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

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

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

Conformational Selection and Induced Fit in Specific Antibody and Antigen Recognition: SPE7 as a Case Study

(2013) Wei Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

(2013) Amelie Stein et al.   PLoS One

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

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

Human Germline Antibody Gene Segments Encode Polyspecific Antibodies

(2013) Jordan R. Willis et al.   PLoS Computational Biology

Protein Dynamics and the Diversity of an Antibody Response

(2012) Ramkrishna Adhikary et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CDR-H3 Diversity Is Not Required for Antigen Recognition by Synthetic Antibodies

(2012) Helena Persson et al.   JOURNAL OF MOLECULAR BIOLOGY

Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody

(2012) A. G. Schmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computer-aided antibody design

(2012) D. Kuroda et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Introduction to current and future protein therapeutics: A protein engineering perspective

(2011) Paul J. Carter   EXPERIMENTAL CELL RESEARCH

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

(2011) Yusuke Naritomi et al.   JOURNAL OF CHEMICAL PHYSICS

A challenging system: Free energy prediction for factor Xa

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

Antibody modeling assessment

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

Metadynamics

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

A New Clustering of Antibody CDR Loop Conformations

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

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Intrinsic Contributions of Tyrosine, Serine, Glycine and Arginine to the Affinity and Specificity of Antibodies

(2008) Sara Birtalan et al.   JOURNAL OF MOLECULAR BIOLOGY

Systematic classification of CDR-L3 in antibodies: Implications of the light chain subtypes and the VL-VH interface

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

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

(2008) Paul Labute   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility

(2008) Mariana Babor 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

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS