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

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

Metadynamics Enhanced Markov Modeling of Protein Dynamics

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

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

Antibodies to watch in 2017

(2016) Janice M. Reichert   mAbs

Length-independent structural similarities enrich the antibody CDR canonical class model

(2016) Jaroslaw Nowak et al.   mAbs

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

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

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

Structural evidence for a constrained conformation of short CDR-L3 in antibodies

(2014) Alexey Teplyakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

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

Computer-aided antibody design

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

Python for Scientists and Engineers

(2011) K. Jarrod Millman et al.   COMPUTING IN SCIENCE & ENGINEERING

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

(2011) Anna Chailyan et al.   FEBS Journal

Molecular Determinants for Antibody Binding on Group 1 House Dust Mite Allergens

(2011) Maksymilian Chruszcz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

A New Clustering of Antibody CDR Loop Conformations

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

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

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

Therapeutic antibodies: successes, limitations and hopes for the future

(2009) Patrick Chames et al.   BRITISH JOURNAL OF PHARMACOLOGY

Epitope Mapping of Anti-Interleukin-13 Neutralizing Antibody CNTO607

(2009) Alexey Teplyakov et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural basis of activation-dependent binding of ligand-mimetic antibody AL-57 to integrin LFA-1

(2009) H. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PIGS: automatic prediction of antibody structures

(2008) P. Marcatili et al.   BIOINFORMATICS

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

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