Related references
Note: Only part of the references are listed.Variational Approach for Learning Markov Processes from Time Series Data
Hao Wu et al.
JOURNAL OF NONLINEAR SCIENCE (2020)
T-Cell Receptor Variable β Domains Rigidify During Affinity Maturation
Monica L. Fernandez-Quintero et al.
SCIENTIFIC REPORTS (2020)
Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin
Ursula Kahler et al.
BIOPHYSICAL JOURNAL (2020)
T-Cell Receptor CDR3 Loop Conformations in Solution Shift the Relative Vα-Vβ Domain Distributions
Monica L. Fernandez-Quintero et al.
FRONTIERS IN IMMUNOLOGY (2020)
Local and Global Rigidification Upon Antibody Affinity Maturation
Monica L. Fernandez-Quintero et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2020)
Antibodies exhibit multiple paratope states influencing VH-VL domain orientations
Monica L. Fernandez-Quintero et al.
COMMUNICATIONS BIOLOGY (2020)
Antibody CDR loops as ensembles in solution vs. canonical clusters from X-ray structures
Monica L. Fernandez-Quintero et al.
MABS (2020)
CDR-H3 loop ensemble in solution - conformational selection upon antibody binding
Monica L. Fernandez-Quintero et al.
MABS (2019)
Shark IgNAR-derived binding domains as potential diagnostic and therapeutic agents
Hanover Matz et al.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY (2019)
Antibody humanization-the Influence of the antibody framework on the CDR-H3 loop ensemble in solution
Monica L. Fernandez-Quintero et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2019)
Characterizing the Diversity CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Ending Properties
Monica L. Fernandez-Quintero et al.
FRONTIERS IN IMMUNOLOGY (2019)
Conformational selection of allergen-antibody complexes-surface plasticity of paratopes and epitopes
Monica L. Fernandez-Quintero et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2019)
Metadynamics Enhanced Markov Modeling of Protein Dynamics
Mithun Biswas et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size
Krystel El Hage et al.
ELIFE (2018)
A cold-blooded view of adaptive immunity
Martin F. Flajnik
NATURE REVIEWS IMMUNOLOGY (2018)
Dynamics behind affinity maturation of an anti-HCMV antibody family influencing antigen binding
Francesco Di Palma et al.
FEBS LETTERS (2017)
Hierarchical Time-Lagged Independent Component Analysis: Computing Slow Modes and Reaction Coordinates for Large Molecular Systems
Guillermo Perez-Hernandez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Special Solutions of the Chapman-Kolmogorov Equation for Multidimensional- State Markov Processes with Continuous Time
R. N. Miroshin
VESTNIK ST PETERSBURG UNIVERSITY-MATHEMATICS (2016)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
Martin K. Scherer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Structural insights and biomedical potential of IgNAR scaffolds from sharks
Stefan Zielonka et al.
MABS (2015)
PLUMED 2: New feathers for an old bird
Gareth A. Tribello et al.
COMPUTER PHYSICS COMMUNICATIONS (2014)
Markov state models of biomolecular conformational dynamics
John D. Chodera et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge
Jochen S. Hub et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins
Matthias J. Feige et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Sander Pronk et al.
BIOINFORMATICS (2013)
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
Romelia Salomon-Ferrer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Well-Tempered Metadynamics as a Tool for Characterizing Multi-Component, Crystalline Molecular Machines
Andrew J. Ilott et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody
Aaron G. Schmidt et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Fuzzy spectral clustering by PCCA plus : application to Markov state models and data classification
Susanna Roeblitz et al.
ADVANCES IN DATA ANALYSIS AND CLASSIFICATION (2013)
Shark Variable New Antigen Receptor (VNAR) Single Domain Antibody Fragments: Stability and Diagnostic Applications
Katherine Griffiths et al.
ANTIBODIES (2013)
A Challenging System: Free Energy Prediction for Factor Xa
Hannes G. Wallnoefer et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Metadynamics
Alessandro Barducci et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)
Linking Well-Tempered Metadynamics Simulations with Experiments
Alessandro Barducci et al.
BIOPHYSICAL JOURNAL (2010)
Origin and evolution of the adaptive immune system: genetic events and selective pressures
Martin F. Flajnik et al.
NATURE REVIEWS GENETICS (2010)
The Importance of Being Tyrosine: Lessons in Molecular Recognition from Minimalist Synthetic Binding Proteins
Shohei Koide et al.
ACS CHEMICAL BIOLOGY (2009)
Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions
James R. Horn et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
Paul Labute
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Well-tempered metadynamics: A smoothly converging and tunable free-energy method
Alessandro Barducci et al.
PHYSICAL REVIEW LETTERS (2008)
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
Alessandro Laio et al.
REPORTS ON PROGRESS IN PHYSICS (2008)
Critical contribution of VH-VL interaction to reshaping of an antibody: The case of humanization of anti-lysozyme antibody, HyHEL-10
Takeshi Nakanishi et al.
PROTEIN SCIENCE (2008)
Maturation of shark single-domain (IgNAR) antibodies: Evidence for induced-fit binding
Robyn L. Stanfield et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Energy landscape and transition state of protein-protein association
Ramzi Alsallaq et al.
BIOPHYSICAL JOURNAL (2007)
An evolutionarily mobile antigen receptor variable region gene: Doubly rearranging NAR-TcR genes in sharks
MF Criscitiello et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
The evolution of adaptive immune systems
MD Cooper et al.
CELL (2006)
Antibody repertoire development in cartilaginous fish
H Dooley et al.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY (2006)
Structure of a shark IgNAR antibody variable domain and modeling of an early-developmental isotype
VA Streltsov et al.
PROTEIN SCIENCE (2005)
Electrostatic potential of aminoacyl-tRNA synthetase navigates tRNA on its pathway to the binding site
D Tworowski et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
Crystal structure of a shark single-domain antibody V region in complex with lysozyme
RL Stanfield et al.
SCIENCE (2004)
Structural analysis, selection, and ontogeny of the shark new antigen receptor (IgNAR): identification of a new locus preferentially expressed in early development
M Diaz et al.
IMMUNOGENETICS (2002)
Experimental assignment of the structure of the transition state for the association of barnase and barstar
C Frisch et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
A shark antibody heavy chain encoded by a nonsomatically rearranged VDJ is preferentially expressed in early development and is convergent with mammalian IgG
LL Rumfelt et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Electrostatic aspects of protein-protein interactions
FB Sheinerman et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2000)
Kinetics of desolvation-mediated protein-protein binding
CJ Camacho et al.
BIOPHYSICAL JOURNAL (2000)
Share Paper
