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)

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)

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)

PeptX: Using Genetic Algorithms to optimize peptides for MHC binding. - Bernhard Knapp; Verena Giczi; Reiner Ribarics; Wolfgang Schreiner (BMC Bioinform., 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)

Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations. - Wolfgang Schreiner; Rudolf Karch; Bernhard Knapp; Nevena Ilieva (Comput. Math. Methods Medicine, 2012)

MH2c: Characterization of major histocompatibility α-helices - an information criterion approach. - Birgit Hischenhuber; Florian Frommlet; Wolfgang Schreiner; Bernhard Knapp (Comput. Phys. Commun., 2012)

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)

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)

Gro2mat: A package to efficiently read gromacs output in MATLAB. - Hung Dien; Charlotte M. Deane; Bernhard Knapp (J. Comput. Chem., 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)

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)

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)

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; et al. (PLoS Comput. Biol., 2014)

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)

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; et al. (PLoS Comput. Biol., 2015)

Progress and challenges in predicting protein interfaces. - Reyhaneh Esmaielbeiki; Konrad Krawczyk; Bernhard Knapp; Jean-Christophe Nebel; Charlotte M. Deane (Briefings Bioinform., 2016)

Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo. - Bernhard Knapp; Samuel Demharter; Charlotte M. Deane; Peter Minary (Bioinform., 2016)

T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex. - Bernhard Knapp; Charlotte M. Deane (J. Chem. Inf. Model., 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)

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; et al. (PLoS Comput. Biol., 2017)

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)

In silico structural modeling of multiple epigenetic marks on DNA. - Konrad Krawczyk; Samuel Demharter; Bernhard Knapp; Charlotte M. Deane; Peter Minary (Bioinform., 2018)

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)

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)

Why current rain denoising models fail on CycleGAN created rain images in autonomous driving. - Michael Kranl; Hubert Ramsauer; Bernhard Knapp (CoRR, 2023)