Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4. - Christoph A. Sotriffer; Rudolf H. Winger; Klaus R. Liedl; Bernd M. Rode; Janos M. Varga (J. Comput. Aided Mol. Des., 1996)

Bidirectional molecular dynamics: Interpretation in terms of a modern formulation of classical mechanics. - Teerakiat Kerdcharoen; Klaus R. Liedl; Bernd M. Rode (J. Comput. Chem., 1996)

Different electrostatic descriptors in comparative molecular field analysis: A comparison of molecular electrostatic and coulomb potentials. - Romano T. Kroemer; Peter Hecht; Klaus R. Liedl (J. Comput. Chem., 1996)

Comparative molecular field analysis of artemisinin derivatives: Ab initio versus semiempirical optimized structures. - Somsak Tonmunphean; Sirirat Kokpol; Vudhichai Parasuk; Peter Wolschann; Rudolf H. Winger; Klaus R. Liedl; Bernd M. Rode (J. Comput. Aided Mol. Des., 1998)

Application of multivariate data analysis methods to Comparative Molecular Field Analysis (CoMFA) data: Proton affinities and pKa prediction for nucleic acids components. - Raimundo Gargallo; Christoph A. Sotriffer; Klaus R. Liedl; Bernd M. Rode (J. Comput. Aided Mol. Des., 1999)

Calculation of sequence-dependent free energies of hydration of dipeptides formed by alanine and glycine. - Hannes H. Loeffler; Christoph A. Sotriffer; Rudolf H. Winger; Klaus R. Liedl; Bernd M. Rode (J. Comput. Chem., 2001)

A QM-MM interface between CHARMM and TURBOMOLE: Implementation and application to systems in bulk phase and biologically active systems. - Markus J. Loferer; Hannes H. Loeffler; Klaus R. Liedl (J. Comput. Chem., 2003)

Extended method for adiabatic mode reordering. - Christofer S. Tautermann; Andreas F. Voegele; Thomas Loerting; Peter Kaps; Klaus R. Liedl (J. Comput. Chem., 2003)

DNA Minor Groove Pharmacophores Describing Sequence Specific Properties. - Gudrun M. Spitzer; Bernd Wellenzohn; Christian Laggner; Thierry Langer; Klaus R. Liedl (J. Chem. Inf. Model., 2007)

How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information. - Johannes Kirchmair; Simona Distinto; Patrick Markt; Daniela Schuster 001; Gudrun M. Spitzer; Klaus R. Liedl; Gerhard Wolber (J. Chem. Inf. Model., 2009)

Theoretical Prediction of Hydrogen Bond Strength for Use in Molecular Modeling. - Monika Nocker; Sandra Handschuh; Christofer S. Tautermann; Klaus R. Liedl (J. Chem. Inf. Model., 2009)

Hydrogen-Bonding Patterns of Minor Groove-Binder-DNA Complexes Reveal Criteria for Discovery of New Scaffolds. - Gudrun M. Spitzer; Bernd Wellenzohn; Patrick Markt; Johannes Kirchmair; Thierry Langer; Klaus R. Liedl (J. Chem. Inf. Model., 2009)

One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space. - Gudrun M. Spitzer; Mathias Heiss; Martina Mangold; Patrick Markt; Johannes Kirchmair; Gerhard Wolber; Klaus R. Liedl (J. Chem. Inf. Model., 2010)

Qualitative prediction of blood-brain barrier permeability on a large and refined dataset. - Markus Muehlbacher; Gudrun M. Spitzer; Klaus R. Liedl; Johannes Kornhuber (J. Comput. Aided Mol. Des., 2011)

A challenging system: Free energy prediction for factor Xa. - Hannes G. Wallnoefer; Klaus R. Liedl; Thomas Fox (J. Comput. Chem., 2011)

Backbone flexibility controls the activity and specificity of a protein-protein interface - specificity in snake venom metalloproteases (SVMPs). - Hannes G. Wallnoefer; Torsten Lingott; José Gutiérrez; Irmgard Merfort; Klaus R. Liedl (J. Cheminformatics, 2011)

Minor Groove Binders and Drugs Targeting Proteins Cover Complementary Regions in Chemical Shape Space. - Julian E. Fuchs; Gudrun M. Spitzer; Ameera Javed; Adam Biela; Christoph Kreutz; Bernd Wellenzohn; Klaus R. Liedl (J. Chem. Inf. Model., 2011)

A GRID-Derived Water Network Stabilizes Molecular Dynamics Computer Simulations of a Protease. - Hannes G. Wallnoefer; Klaus R. Liedl; Thomas Fox (J. Chem. Inf. Model., 2011)

Identification of Novel Liver X Receptor Activators by Structure-Based Modeling. - Susanne von Grafenstein; Judit Mihaly-Bison; Gerhard Wolber; Valery N. Bochkov; Klaus R. Liedl; Daniela Schuster 001 (J. Chem. Inf. Model., 2012)

Substrate Sequences Tell Similar Stories as Binding Cavities: Commentary. - Julian E. Fuchs; Klaus R. Liedl (J. Chem. Inf. Model., 2013)

Deriving Static Atomic Multipoles from the Electrostatic Potential. - Christian Kramer; Tristan Bereau; Alexander Spinn; Klaus R. Liedl; Peter Gedeck; Markus Meuwly (J. Chem. Inf. Model., 2013)

Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos. - Julian E. Fuchs; Susanne von Grafenstein; Roland G. Huber; Christian Kramer; Klaus R. Liedl (PLoS Comput. Biol., 2013)

Cleavage Entropy as Quantitative Measure of Protease Specificity. - Julian E. Fuchs; Susanne von Grafenstein; Roland G. Huber; Michael A. Margreiter; Gudrun M. Spitzer; Hannes G. Wallnoefer; Klaus R. Liedl (PLoS Comput. Biol., 2013)

Limits to molecular matched-pair analysis: the experimental uncertainty case. - Christian Kramer; Klaus R. Liedl (J. Cheminformatics, 2014)

Entropy in specificity and thermodynamics of binding. - Klaus R. Liedl (J. Cheminformatics, 2014)

Heteroaromatic π-Stacking Energy Landscapes. - Roland G. Huber; Michael A. Margreiter; Julian E. Fuchs; Susanne von Grafenstein; Christofer S. Tautermann; Klaus R. Liedl; Thomas Fox (J. Chem. Inf. Model., 2014)

Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications. - Julian E. Fuchs; Bernd Wellenzohn; Nils Weskamp; Klaus R. Liedl (J. Chem. Inf. Model., 2015)

Strong Nonadditivity as a Key Structure-Activity Relationship Feature: Distinguishing Structural Changes from Assay Artifacts. - Christian Kramer; Julian E. Fuchs; Klaus R. Liedl (J. Chem. Inf. Model., 2015)

Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design. - Johannes R. Loeffler; Emanuel S. R. Ehmki; Julian E. Fuchs; Klaus R. Liedl (J. Comput. Aided Mol. Des., 2016)

Protease Inhibitors in View of Peptide Substrate Databases. - Birgit J. Waldner; Julian E. Fuchs; Michael Schauperl; Christian Kramer; Klaus R. Liedl (J. Chem. Inf. Model., 2016)

Binding Pose Flip Explained via Enthalpic and Entropic Contributions. - Michael Schauperl; Paul Czodrowski; Julian E. Fuchs; Roland G. Huber; Birgit J. Waldner; Maren Podewitz; Christian Kramer; Klaus R. Liedl (J. Chem. Inf. Model., 2017)

Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization. - Anna S. Kamenik; Uta F. Lessel; Julian E. Fuchs; Thomas Fox; Klaus R. Liedl (J. Chem. Inf. Model., 2018)

Hydration of Aromatic Heterocycles as an Adversary of π-Stacking. - Johannes R. Loeffler; Michael Schauperl; Klaus R. Liedl (J. Chem. Inf. Model., 2019)

Understanding Structure-Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations. - Lucianna Helene Santos; Birgit J. Waldner; Julian E. Fuchs; Glaécia A. N. Pereira; Klaus R. Liedl; Ernesto Raúl Caffarena; Rafaela Salgado Ferreira (J. Chem. Inf. Model., 2019)

Catalytic Site pKa Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations. - Florian Hofer 002; Johannes Kraml; Ursula Kahler; Anna S. Kamenik; Klaus R. Liedl (J. Chem. Inf. Model., 2020)

Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments. - Anna S. Kamenik; Johannes Kraml; Florian Hofer 002; Franz Waibl; Patrick K. Quoika; Ursula Kahler; Michael Schauperl; Klaus R. Liedl (J. Chem. Inf. Model., 2020)

Solvation Thermodynamics in Different Solvents: Water-Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory. - Johannes Kraml; Florian Hofer 002; Anna S. Kamenik; Franz Waibl; Ursula Kahler; Michael Schauperl; Klaus R. Liedl (J. Chem. Inf. Model., 2020)

STACKED - Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding. - Johannes R. Loeffler; Monica L. Fernández-Quintero; Michael Schauperl; Klaus R. Liedl (J. Chem. Inf. Model., 2020)

X-Entropy: A Parallelized Kernel Density Estimator with Automated Bandwidth Selection to Calculate Entropy. - Johannes Kraml; Florian Hofer 002; Patrick K. Quoika; Anna S. Kamenik; Klaus R. Liedl (J. Chem. Inf. Model., 2021)

pyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules. - Mayk C. Ramos; Patrick K. Quoika; Vitor A. C. Horta; Douglas Mota Dias; Elan G. Costa; Jorge Luís Machado do Amaral; Luigi M. Ribeiro; Klaus R. Liedl; Bruno A. C. Horta (J. Chem. Inf. Model., 2021)

Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures. - Franz Waibl; Johannes Kraml; Monica L. Fernández-Quintero; Johannes R. Loeffler; Klaus R. Liedl (J. Comput. Aided Mol. Des., 2022)

Structural mechanism of Fab domain dissociation as a measure of interface stability. - Nancy D. Pomarici; Franz Waibl; Patrick K. Quoika; Alexander Bujotzek; Guy Georges; Monica L. Fernández-Quintero; Klaus R. Liedl (J. Comput. Aided Mol. Des., 2023)

PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability. - Valentin J. Hoerschinger; Franz Waibl; Nancy D. Pomarici; Johannes R. Loeffler; Charlotte M. Deane; Guy Georges; Hubert Kettenberger; Monica L. Fernández-Quintero; Klaus R. Liedl (J. Chem. Inf. Model., 2023)

Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity. - Xuechen Tang; Janik Kokot; Franz Waibl; Monica L. Fernández-Quintero; Anna S. Kamenik; Klaus R. Liedl (J. Chem. Inf. Model., 2023)

From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4. - Vera A. Spanke; Valentin J. Hoerschinger; Veronika Ruzsanyi; Klaus R. Liedl (J. Comput. Aided Mol. Des., 2025)