Bernhard Knapp

26 papers Journal 26
YearRankTypeTitle / Venue / Authors
2023 J jnl
Why current rain denoising models fail on CycleGAN created rain images in autonomous driving.
CoRR
Michael Kranl, Hubert Ramsauer, Bernhard Knapp
2019 J jnl
HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo.
J. Chem. Inf. Model.
Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary
2019 J jnl
MHC binding affects the dynamics of different T-cell receptors in different ways.
PLoS Comput. Biol.
Bernhard Knapp, P. Anton van der Merwe, Omer Dushek, Charlotte M. Deane
2018 J jnl
In silico structural modeling of multiple epigenetic marks on DNA.
Bioinform.
Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary
2018 J jnl
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions.
Bioinform.
Bernhard Knapp, Marta Alcalá, Hao Zhang, Clare E. West, P. Anton van der Merwe, Charlotte M. Deane
2017 J jnl
Ten simple rules for surviving an interdisciplinary PhD.
PLoS Comput. Biol.
Samuel Demharter, Nicholas Pearce, Kylie Beattie, Isabel Frost, Jinwoo Leem, Alistair Martin, Robert Oppenheimer, Cristian Regep, Tammo Rukat, Alexander Skates, Nicola Trendel, David J. Gavaghan, Charlotte M. Deane, Bernhard Knapp
2016 J jnl
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.
Bioinform.
Bernhard Knapp, Samuel Demharter, Charlotte M. Deane, Peter Minary
2016 J jnl
Progress and challenges in predicting protein interfaces.
Briefings Bioinform.
Reyhaneh Esmaielbeiki, Konrad Krawczyk, Bernhard Knapp, Jean-Christophe Nebel, Charlotte M. Deane
2016 J jnl
T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex.
J. Chem. Inf. Model.
Bernhard Knapp, Charlotte M. Deane
2016 J jnl
Tertiary Element Interaction in HIV-1 TAR.
J. Chem. Inf. Model.
Konrad Krawczyk, Adelene Y. L. Sim, Bernhard Knapp, Charlotte M. Deane, Peter Minary
2015 J jnl
Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations.
Briefings Bioinform.
Bernhard Knapp, Samuel Demharter, Reyhaneh Esmaielbeiki, Charlotte M. Deane
2015 J jnl
Ten Simple Rules for a Successful Cross-Disciplinary Collaboration.
PLoS Comput. Biol.
Bernhard Knapp, Rémi Bardenet, Miguel O. Bernabeu, Rafel Bordas, Maria Bruna, Ben Calderhead, Jonathan Cooper, Alexander G. Fletcher, Derek Groen, Bram Kuijper, Joanna Lewis, Greg J. McInerny, Timo Minssen, James M. Osborne, Verena Paulitschke, Joe Pitt-Francis, Jelena Todoric, Christian A. Yates, David Gavaghan, Charlotte M. Deane
2014 J jnl
Crowdsourcing Yields a New Standard for Kinks in Protein Helices.
J. Chem. Inf. Model.
Henry R. Wilman, Jean-Paul Ebejer, Jiye Shi, Charlotte M. Deane, Bernhard Knapp
2014 J jnl
Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design.
PLoS Comput. Biol.
James Dunbar, Bernhard Knapp, Angelika Fuchs, Jiye Shi, Charlotte M. Deane
2014 J jnl
Gro2mat: A package to efficiently read gromacs output in MATLAB.
J. Comput. Chem.
Hung Dien, Charlotte M. Deane, Bernhard Knapp
2014 J jnl
Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study.
PLoS Comput. Biol.
Bernhard Knapp, James Dunbar, Charlotte M. Deane
2014 J jnl
Ten Simple Rules for Effective Computational Research.
PLoS Comput. Biol.
James M. Osborne, Miguel O. Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G. Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J. McInerny, Gary R. Mirams, Joe Pitt-Francis, Biswa Sengupta, David W. Wright, Christian A. Yates, David Gavaghan, Stephen Emmott, Charlotte M. Deane
2013 J jnl
Corrigendum: Differential geometric analysis of alterations in MH α-helices.
J. Comput. Chem.
Birgit Hischenhuber, Hans Havlicek, Jelena Todoric, Sonja Höllrigl-Binder, Wolfgang Schreiner, Bernhard Knapp
2013 J jnl
Differential geometric analysis of alterations in MH α-helices.
J. Comput. Chem.
Birgit Hischenhuber, Hans Havlicek, Jelena Todoric, Sonja Höllrigl-Binder, Wolfgang Schreiner, Bernhard Knapp
2012 J jnl
MH
Comput. Phys. Commun.
Birgit Hischenhuber, Florian Frommlet, Wolfgang Schreiner, Bernhard Knapp
2012 J jnl
Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations.
Comput. Math. Methods Medicine
Wolfgang Schreiner, Rudolf Karch, Bernhard Knapp, Nevena Ilieva
2011 J jnl
Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible?
J. Comput. Biol.
Bernhard Knapp, Sophie Frantal, Michael Cibena, Wolfgang Schreiner, P. Bauer
2011 J jnl
PeptX: Using Genetic Algorithms to optimize peptides for MHC binding.
BMC Bioinform.
Bernhard Knapp, Verena Giczi, Reiner Ribarics, Wolfgang Schreiner
2010 J jnl
vmdICE: A plug-in for rapid evaluation of molecular dynamics simulations using VMD.
J. Comput. Chem.
Bernhard Knapp, Nadja Lederer, Ulrich Omasits, Wolfgang Schreiner
2009 J jnl
A critical cross-validation of high throughput structural binding prediction methods for pMHC.
J. Comput. Aided Mol. Des.
Bernhard Knapp, Ulrich Omasits, Sophie Frantal, Wolfgang Schreiner
2009 J jnl
jSimMacs for GROMACS: A Java Application for Advanced Molecular Dynamics Simulations with Remote Access Capability.
J. Chem. Inf. Model.
Sanjit Roopra, Bernhard Knapp, Ulrich Omasits, Wolfgang Schreiner