Bernhard Knapp

According to our database, Bernhard Knapp authored at least 26 papers between 2009 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

Why current rain denoising models fail on CycleGAN created rain images in autonomous driving.

Michael Kranl, Hubert Ramsauer, Bernhard Knapp

CoRR, 2023

2019

MHC binding affects the dynamics of different T-cell receptors in different ways.

Bernhard Knapp, P. Anton van der Merwe, Omer Dushek, Charlotte M. Deane

PLoS Comput. Biol., 2019

HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo.

Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary

J. Chem. Inf. Model., 2019

2018

In silico structural modeling of multiple epigenetic marks on DNA.

Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary

Bioinform., 2018

pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions.

Bernhard Knapp, Marta Alcalá, Hao Zhang, Clare E. West, P. Anton van der Merwe, Charlotte M. Deane

Bioinform., 2018

2017

Ten simple rules for surviving an interdisciplinary PhD.

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

PLoS Comput. Biol., 2017

2016

Tertiary Element Interaction in HIV-1 TAR.

Konrad Krawczyk, Adelene Y. L. Sim, Bernhard Knapp, Charlotte M. Deane, Peter Minary

J. Chem. Inf. Model., 2016

T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex.

Bernhard Knapp, Charlotte M. Deane

J. Chem. Inf. Model., 2016

Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.

Bernhard Knapp, Samuel Demharter, Charlotte M. Deane, Peter Minary

Bioinform., 2016

Progress and challenges in predicting protein interfaces.

Reyhaneh Esmaielbeiki, Konrad Krawczyk, Bernhard Knapp, Jean-Christophe Nebel, Charlotte M. Deane

Briefings Bioinform., 2016

2015

Ten Simple Rules for a Successful Cross-Disciplinary Collaboration.

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

PLoS Comput. Biol., 2015

Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations.

Bernhard Knapp, Samuel Demharter, Reyhaneh Esmaielbeiki, Charlotte M. Deane

Briefings Bioinform., 2015

2014

Ten Simple Rules for Effective Computational Research.

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

PLoS Comput. Biol., 2014

Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study.

Bernhard Knapp, James Dunbar, Charlotte M. Deane

PLoS Comput. Biol., 2014

Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design.

James Dunbar, Bernhard Knapp, Angelika Fuchs, Jiye Shi, Charlotte M. Deane

PLoS Comput. Biol., 2014

Crowdsourcing Yields a New Standard for Kinks in Protein Helices.

Henry R. Wilman, Jean-Paul Ebejer, Jiye Shi, Charlotte M. Deane, Bernhard Knapp

J. Chem. Inf. Model., 2014

Gro2mat: A package to efficiently read gromacs output in MATLAB.

Hung Dien, Charlotte M. Deane, Bernhard Knapp

J. Comput. Chem., 2014

2013

Corrigendum: Differential geometric analysis of alterations in MH α-helices.

Birgit Hischenhuber, Hans Havlicek, Jelena Todoric, Sonja Höllrigl-Binder, Wolfgang Schreiner, Bernhard Knapp

J. Comput. Chem., 2013

Differential geometric analysis of alterations in MH α-helices.

Birgit Hischenhuber, Hans Havlicek, Jelena Todoric, Sonja Höllrigl-Binder, Wolfgang Schreiner, Bernhard Knapp

J. Comput. Chem., 2013

2012

MH²c: Characterization of major histocompatibility α-helices - an information criterion approach.

Birgit Hischenhuber, Florian Frommlet, Wolfgang Schreiner, Bernhard Knapp

Comput. Phys. Commun., 2012

Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations.

Wolfgang Schreiner, Rudolf Karch, Bernhard Knapp, Nevena Ilieva

Comput. Math. Methods Medicine, 2012

2011

Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible?

Bernhard Knapp, Sophie Frantal, Michael Cibena, Wolfgang Schreiner, P. Bauer

J. Comput. Biol., 2011

PeptX: Using Genetic Algorithms to optimize peptides for MHC binding.

Bernhard Knapp, Verena Giczi, Reiner Ribarics, Wolfgang Schreiner

BMC Bioinform., 2011

2010

vmdICE: A plug-in for rapid evaluation of molecular dynamics simulations using VMD.

Bernhard Knapp, Nadja Lederer, Ulrich Omasits, Wolfgang Schreiner

J. Comput. Chem., 2010

2009

jSimMacs for GROMACS: A Java Application for Advanced Molecular Dynamics Simulations with Remote Access Capability.

Sanjit Roopra, Bernhard Knapp, Ulrich Omasits, Wolfgang Schreiner

J. Chem. Inf. Model., 2009

A critical cross-validation of high throughput structural binding prediction methods for pMHC.

Bernhard Knapp, Ulrich Omasits, Sophie Frantal, Wolfgang Schreiner

J. Comput. Aided Mol. Des., 2009