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ORCIDBernhard Knapp
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2020 – today
- 2023
[i1]Michael Kranl, Hubert Ramsauer, Bernhard Knapp:
Why current rain denoising models fail on CycleGAN created rain images in autonomous driving. CoRR abs/2305.12983 (2023)
2010 – 2019
- 2019
- [j25]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): 2894-2899 (2019) - [j24]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) - 2018
- [j23]Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary:
In silico structural modeling of multiple epigenetic marks on DNA. Bioinform. 34(1): 41-48 (2018) - [j22]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): 1941-1943 (2018) - 2017
- [j21]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) - 2016
- [j20]Reyhaneh Esmaielbeiki, Konrad Krawczyk, Bernhard Knapp, Jean-Christophe Nebel, Charlotte M. Deane:
Progress and challenges in predicting protein interfaces. Briefings Bioinform. 17(1): 117-131 (2016) - [j19]Bernhard Knapp, Samuel Demharter, Charlotte M. Deane, Peter Minary:
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo. Bioinform. 32(2): 181-186 (2016) - [j18]Bernhard Knapp, Charlotte M. Deane:
T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex. J. Chem. Inf. Model. 56(1): 46-53 (2016) - [j17]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): 1746-1754 (2016) - 2015
- [j16]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): 1035-1044 (2015) - [j15]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) - 2014
- [j14]Hung Dien, Charlotte M. Deane, Bernhard Knapp:
Gro2mat: A package to efficiently read gromacs output in MATLAB. J. Comput. Chem. 35(20): 1528-1531 (2014) - [j13]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): 2585-2593 (2014) - [j12]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) - [j11]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) - [j10]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) - 2013
- [j9]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): 1862-1879 (2013) - [j8]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): 2834 (2013) - 2012
- [j7]Wolfgang Schreiner, Rudolf Karch, Bernhard Knapp, Nevena Ilieva:
Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations. Comput. Math. Methods Medicine 2012: 173521:1-173521:9 (2012) - [j6]Birgit Hischenhuber, Florian Frommlet, Wolfgang Schreiner, Bernhard Knapp:
MH2c: Characterization of major histocompatibility α-helices - an information criterion approach. Comput. Phys. Commun. 183(7): 1481-1490 (2012) - 2011
- [j5]Bernhard Knapp, Verena Giczi, Reiner Ribarics, Wolfgang Schreiner:
PeptX: Using Genetic Algorithms to optimize peptides for MHC binding. BMC Bioinform. 12: 241 (2011) - [j4]Bernhard Knapp, Sophie Frantal, Michael 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): 997-1005 (2011) - 2010
- [j3]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): 2868-2873 (2010)
2000 – 2009
- 2009
- [j2]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): 301-307 (2009) - [j1]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): 2412-2417 (2009)
Coauthor Index
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