Klaus R. Liedl

45 papers Journal 45

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4. J. Comput. Aided Mol. Des. Vera A. Spanke, Valentin J. Hoerschinger, Veronika Ruzsanyi, Klaus R. Liedl
2023	J	`jnl`	Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity. J. Chem. Inf. Model. Xuechen Tang, Janik Kokot, Franz Waibl, Monica L. Fernández-Quintero, Anna S. Kamenik, Klaus R. Liedl
2023	J	`jnl`	PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability. J. Chem. Inf. Model. 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
2023	J	`jnl`	Structural mechanism of Fab domain dissociation as a measure of interface stability. J. Comput. Aided Mol. Des. Nancy D. Pomarici, Franz Waibl, Patrick K. Quoika, Alexander Bujotzek, Guy Georges, Monica L. Fernández-Quintero, Klaus R. Liedl
2022	J	`jnl`	Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures. J. Comput. Aided Mol. Des. Franz Waibl, Johannes Kraml, Monica L. Fernández-Quintero, Johannes R. Loeffler, Klaus R. Liedl
2021	J	`jnl`	X-Entropy: A Parallelized Kernel Density Estimator with Automated Bandwidth Selection to Calculate Entropy. J. Chem. Inf. Model. Johannes Kraml, Florian Hofer, Patrick K. Quoika, Anna S. Kamenik, Klaus R. Liedl
2021	J	`jnl`	pyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules. J. Chem. Inf. Model. 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
2020	J	`jnl`	Catalytic Site pKa Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations. J. Chem. Inf. Model. Florian Hofer, Johannes Kraml, Ursula Kahler, Anna S. Kamenik, Klaus R. Liedl
2020	J	`jnl`	Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments. J. Chem. Inf. Model. Anna S. Kamenik, Johannes Kraml, Florian Hofer, Franz Waibl, Patrick K. Quoika, Ursula Kahler, Michael Schauperl, Klaus R. Liedl
2020	J	`jnl`	STACKED - Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding. J. Chem. Inf. Model. Johannes R. Loeffler, Monica L. Fernández-Quintero, Michael Schauperl, Klaus R. Liedl
2020	J	`jnl`	Solvation Thermodynamics in Different Solvents: Water-Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory. J. Chem. Inf. Model. Johannes Kraml, Florian Hofer, Anna S. Kamenik, Franz Waibl, Ursula Kahler, Michael Schauperl, Klaus R. Liedl
2019	J	`jnl`	Hydration of Aromatic Heterocycles as an Adversary of π-Stacking. J. Chem. Inf. Model. Johannes R. Loeffler, Michael Schauperl, Klaus R. Liedl
2019	J	`jnl`	Understanding Structure-Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations. J. Chem. Inf. Model. Lucianna Helene Santos, Birgit J. Waldner, Julian E. Fuchs, Glaécia A. N. Pereira, Klaus R. Liedl, Ernesto Raúl Caffarena, Rafaela Salgado Ferreira
2018	J	`jnl`	Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization. J. Chem. Inf. Model. Anna S. Kamenik, Uta F. Lessel, Julian E. Fuchs, Thomas Fox, Klaus R. Liedl
2017	J	`jnl`	Binding Pose Flip Explained via Enthalpic and Entropic Contributions. J. Chem. Inf. Model. Michael Schauperl, Paul Czodrowski, Julian E. Fuchs, Roland G. Huber, Birgit J. Waldner, Maren Podewitz, Christian Kramer, Klaus R. Liedl
2016	J	`jnl`	Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design. J. Comput. Aided Mol. Des. Johannes R. Loeffler, Emanuel S. R. Ehmki, Julian E. Fuchs, Klaus R. Liedl
2016	J	`jnl`	Protease Inhibitors in View of Peptide Substrate Databases. J. Chem. Inf. Model. Birgit J. Waldner, Julian E. Fuchs, Michael Schauperl, Christian Kramer, Klaus R. Liedl
2015	J	`jnl`	Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications. J. Chem. Inf. Model. Julian E. Fuchs, Bernd Wellenzohn, Nils Weskamp, Klaus R. Liedl
2015	J	`jnl`	Strong Nonadditivity as a Key Structure-Activity Relationship Feature: Distinguishing Structural Changes from Assay Artifacts. J. Chem. Inf. Model. Christian Kramer, Julian E. Fuchs, Klaus R. Liedl
2014	J	`jnl`	Entropy in specificity and thermodynamics of binding. J. Cheminformatics Klaus R. Liedl
2014	J	`jnl`	Heteroaromatic π-Stacking Energy Landscapes. J. Chem. Inf. Model. Roland G. Huber, Michael A. Margreiter, Julian E. Fuchs, Susanne von Grafenstein, Christofer S. Tautermann, Klaus R. Liedl, Thomas Fox
2014	J	`jnl`	Limits to molecular matched-pair analysis: the experimental uncertainty case. J. Cheminformatics Christian Kramer, Klaus R. Liedl
2013	J	`jnl`	Cleavage Entropy as Quantitative Measure of Protease Specificity. PLoS Comput. Biol. Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Michael A. Margreiter, Gudrun M. Spitzer, Hannes G. Wallnoefer, Klaus R. Liedl
2013	J	`jnl`	Deriving Static Atomic Multipoles from the Electrostatic Potential. J. Chem. Inf. Model. Christian Kramer, Tristan Bereau, Alexander Spinn, Klaus R. Liedl, Peter Gedeck, Markus Meuwly
2013	J	`jnl`	Substrate Sequences Tell Similar Stories as Binding Cavities: Commentary. J. Chem. Inf. Model. Julian E. Fuchs, Klaus R. Liedl
2013	J	`jnl`	Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos. PLoS Comput. Biol. Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Christian Kramer, Klaus R. Liedl
2012	J	`jnl`	Identification of Novel Liver X Receptor Activators by Structure-Based Modeling. J. Chem. Inf. Model. Susanne von Grafenstein, Judit Mihaly-Bison, Gerhard Wolber, Valery N. Bochkov, Klaus R. Liedl, Daniela Schuster
2011	J	`jnl`	A GRID-Derived Water Network Stabilizes Molecular Dynamics Computer Simulations of a Protease. J. Chem. Inf. Model. Hannes G. Wallnoefer, Klaus R. Liedl, Thomas Fox
2011	J	`jnl`	A challenging system: Free energy prediction for factor Xa. J. Comput. Chem. Hannes G. Wallnoefer, Klaus R. Liedl, Thomas Fox
2011	J	`jnl`	Backbone flexibility controls the activity and specificity of a protein-protein interface - specificity in snake venom metalloproteases (SVMPs). J. Cheminformatics Hannes G. Wallnoefer, Torsten Lingott, José Gutiérrez, Irmgard Merfort, Klaus R. Liedl
2011	J	`jnl`	Minor Groove Binders and Drugs Targeting Proteins Cover Complementary Regions in Chemical Shape Space. J. Chem. Inf. Model. Julian E. Fuchs, Gudrun M. Spitzer, Ameera Javed, Adam Biela, Christoph Kreutz, Bernd Wellenzohn, Klaus R. Liedl
2011	J	`jnl`	Qualitative prediction of blood-brain barrier permeability on a large and refined dataset. J. Comput. Aided Mol. Des. Markus Muehlbacher, Gudrun M. Spitzer, Klaus R. Liedl, Johannes Kornhuber
2010	J	`jnl`	One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space. J. Chem. Inf. Model. Gudrun M. Spitzer, Mathias Heiss, Martina Mangold, Patrick Markt, Johannes Kirchmair, Gerhard Wolber, Klaus R. Liedl
2009	J	`jnl`	How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information. J. Chem. Inf. Model. Johannes Kirchmair, Simona Distinto, Patrick Markt, Daniela Schuster, Gudrun M. Spitzer, Klaus R. Liedl, Gerhard Wolber
2009	J	`jnl`	Hydrogen-Bonding Patterns of Minor Groove-Binder-DNA Complexes Reveal Criteria for Discovery of New Scaffolds. J. Chem. Inf. Model. Gudrun M. Spitzer, Bernd Wellenzohn, Patrick Markt, Johannes Kirchmair, Thierry Langer, Klaus R. Liedl
2009	J	`jnl`	Theoretical Prediction of Hydrogen Bond Strength for Use in Molecular Modeling. J. Chem. Inf. Model. Monika Nocker, Sandra Handschuh, Christofer S. Tautermann, Klaus R. Liedl
2007	J	`jnl`	DNA Minor Groove Pharmacophores Describing Sequence Specific Properties. J. Chem. Inf. Model. Gudrun M. Spitzer, Bernd Wellenzohn, Christian Laggner, Thierry Langer, Klaus R. Liedl
2003	J	`jnl`	A QM-MM interface between CHARMM and TURBOMOLE: Implementation and application to systems in bulk phase and biologically active systems. J. Comput. Chem. Markus J. Loferer, Hannes H. Loeffler, Klaus R. Liedl
2003	J	`jnl`	Extended method for adiabatic mode reordering. J. Comput. Chem. Christofer S. Tautermann, Andreas F. Voegele, Thomas Loerting, Peter Kaps, Klaus R. Liedl
2001	J	`jnl`	Calculation of sequence-dependent free energies of hydration of dipeptides formed by alanine and glycine. J. Comput. Chem. Hannes H. Loeffler, Christoph A. Sotriffer, Rudolf H. Winger, Klaus R. Liedl, Bernd M. Rode
1999	J	`jnl`	Application of multivariate data analysis methods to Comparative Molecular Field Analysis (CoMFA) data: Proton affinities and pKa prediction for nucleic acids components. J. Comput. Aided Mol. Des. Raimundo Gargallo, Christoph A. Sotriffer, Klaus R. Liedl, Bernd M. Rode
1998	J	`jnl`	Comparative molecular field analysis of artemisinin derivatives: Ab initio versus semiempirical optimized structures. J. Comput. Aided Mol. Des. Somsak Tonmunphean, Sirirat Kokpol, Vudhichai Parasuk, Peter Wolschann, Rudolf H. Winger, Klaus R. Liedl, Bernd M. Rode
1996	J	`jnl`	Bidirectional molecular dynamics: Interpretation in terms of a modern formulation of classical mechanics. J. Comput. Chem. Teerakiat Kerdcharoen, Klaus R. Liedl, Bernd M. Rode
1996	J	`jnl`	Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4. J. Comput. Aided Mol. Des. Christoph A. Sotriffer, Rudolf H. Winger, Klaus R. Liedl, Bernd M. Rode, Janos M. Varga
1996	J	`jnl`	Different electrostatic descriptors in comparative molecular field analysis: A comparison of molecular electrostatic and coulomb potentials. J. Comput. Chem. Romano T. Kroemer, Peter Hecht, Klaus R. Liedl