Bernhard Knapp

Publication Activity (10 Years)

Years Active: 2009-2023
Publications (10 Years): 10

Top Topics

Molecular Dynamics

Predicting Protein

Major Histocompatibility Complex

Top Venues

PLoS Comput. Biol.

J. Chem. Inf. Model.

J. Comput. Chem.

Publications

Michael Kranl, Hubert Ramsauer, Bernhard Knapp
Why current rain denoising models fail on CycleGAN created rain images in autonomous driving. CoRR (2023)
Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary
HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo. J. Chem. Inf. Model. 59 (6) (2019)
Bernhard Knapp, P. Anton van der Merwe, Omer Dushek, Charlotte M. Deane
MHC binding affects the dynamics of different T-cell receptors in different ways. PLoS Comput. Biol. 15 (9) (2019)
Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary
In silico structural modeling of multiple epigenetic marks on DNA. Bioinform. 34 (1) (2018)
Bernhard Knapp, Marta Alcalá, Hao Zhang, Clare E. West, P. Anton van der Merwe, Charlotte M. Deane
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions. Bioinform. 34 (11) (2018)
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
Ten simple rules for surviving an interdisciplinary PhD. PLoS Comput. Biol. 13 (5) (2017)
Konrad Krawczyk, Adelene Y. L. Sim, Bernhard Knapp, Charlotte M. Deane, Peter Minary
Tertiary Element Interaction in HIV-1 TAR. J. Chem. Inf. Model. 56 (9) (2016)
Bernhard Knapp, Samuel Demharter, Charlotte M. Deane, Peter Minary
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo. Bioinform. 32 (2) (2016)
Bernhard Knapp, Charlotte M. Deane
T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex. J. Chem. Inf. Model. 56 (1) (2016)
Reyhaneh Esmaielbeiki, Konrad Krawczyk, Bernhard Knapp, Jean-Christophe Nebel, Charlotte M. Deane
Progress and challenges in predicting protein interfaces. Briefings Bioinform. 17 (1) (2016)
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
Ten Simple Rules for a Successful Cross-Disciplinary Collaboration. PLoS Comput. Biol. 11 (4) (2015)
Bernhard Knapp, Samuel Demharter, Reyhaneh Esmaielbeiki, Charlotte M. Deane
Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations. Briefings Bioinform. 16 (6) (2015)
James Dunbar, Bernhard Knapp, Angelika Fuchs, Jiye Shi, Charlotte M. Deane
Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design. PLoS Comput. Biol. 10 (9) (2014)
Hung Dien, Charlotte M. Deane, Bernhard Knapp
Gro2mat: A package to efficiently read gromacs output in MATLAB. J. Comput. Chem. 35 (20) (2014)
Bernhard Knapp, James Dunbar, Charlotte M. Deane
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. 10 (8) (2014)
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
Ten Simple Rules for Effective Computational Research. PLoS Comput. Biol. 10 (3) (2014)
Henry R. Wilman, Jean-Paul Ebejer, Jiye Shi, Charlotte M. Deane, Bernhard Knapp
Crowdsourcing Yields a New Standard for Kinks in Protein Helices. J. Chem. Inf. Model. 54 (9) (2014)
Birgit Hischenhuber, Hans Havlicek, Jelena Todoric, Sonja Höllrigl-Binder, Wolfgang Schreiner, Bernhard Knapp
Differential geometric analysis of alterations in MH α-helices. J. Comput. Chem. 34 (21) (2013)
Birgit Hischenhuber, Hans Havlicek, Jelena Todoric, Sonja Höllrigl-Binder, Wolfgang Schreiner, Bernhard Knapp
Corrigendum: Differential geometric analysis of alterations in MH α-helices. J. Comput. Chem. 34 (32) (2013)
Birgit Hischenhuber, Florian Frommlet, Wolfgang Schreiner, Bernhard Knapp
c: Characterization of major histocompatibility α-helices - an information criterion approach. Comput. Phys. Commun. 183 (7) (2012)
Wolfgang Schreiner, Rudolf Karch, Bernhard Knapp, Nevena Ilieva
Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations. Comput. Math. Methods Medicine 2012 (2012)
Bernhard Knapp, Sophie Frantal, M. Cibena, Wolfgang Schreiner, P. Bauer
Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible? J. Comput. Biol. 18 (8) (2011)
Bernhard Knapp, Verena Giczi, Reiner Ribarics, Wolfgang Schreiner
PeptX: Using Genetic Algorithms to optimize peptides for MHC binding. BMC Bioinform. 12 (2011)
Bernhard Knapp, Nadja Lederer, Ulrich Omasits, Wolfgang Schreiner
vmdICE: A plug-in for rapid evaluation of molecular dynamics simulations using VMD. J. Comput. Chem. 31 (16) (2010)
Bernhard Knapp, Ulrich Omasits, Sophie Frantal, Wolfgang Schreiner
A critical cross-validation of high throughput structural binding prediction methods for pMHC. J. Comput. Aided Mol. Des. 23 (5) (2009)
Sanjit Roopra, Bernhard Knapp, Ulrich Omasits, Wolfgang Schreiner
jSimMacs for GROMACS: A Java Application for Advanced Molecular Dynamics Simulations with Remote Access Capability. J. Chem. Inf. Model. 49 (10) (2009)