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Klaus R. Liedl
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2020 – today
- 2023
- [j44]Nancy D. Pomarici, Franz Waibl, Patrick K. Quoika, Alexander Bujotzek, Guy Georges, Monica L. Fernández-Quintero, Klaus R. Liedl:
Structural mechanism of Fab domain dissociation as a measure of interface stability. J. Comput. Aided Mol. Des. 37(4): 201-215 (2023) - [j43]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
:
PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability. J. Chem. Inf. Model. 63(22): 6964-6971 (2023) - [j42]Xuechen Tang, Janik Kokot, Franz Waibl, Monica L. Fernández-Quintero
, Anna S. Kamenik
, Klaus R. Liedl
:
Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity. J. Chem. Inf. Model. 63(22): 7107-7123 (2023) - 2022
- [j41]Franz Waibl, Johannes Kraml, Monica L. Fernández-Quintero, Johannes R. Loeffler, Klaus R. Liedl
:
Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures. J. Comput. Aided Mol. Des. 36(2): 101-116 (2022) - 2021
- [j40]Johannes Kraml, Florian Hofer, Patrick K. Quoika
, Anna S. Kamenik
, Klaus R. Liedl
:
X-Entropy: A Parallelized Kernel Density Estimator with Automated Bandwidth Selection to Calculate Entropy. J. Chem. Inf. Model. 61(4): 1533-1538 (2021) - [j39]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
:
pyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules. J. Chem. Inf. Model. 61(4): 1539-1544 (2021) - 2020
- [j38]Johannes R. Loeffler
, Monica L. Fernández-Quintero, Michael Schauperl, Klaus R. Liedl
:
STACKED - Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding. J. Chem. Inf. Model. 60(4): 2304-2313 (2020) - [j37]Florian Hofer, Johannes Kraml, Ursula Kahler, Anna S. Kamenik
, Klaus R. Liedl
:
Catalytic Site pKa Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations. J. Chem. Inf. Model. 60(6): 3030-3042 (2020) - [j36]Anna S. Kamenik
, Johannes Kraml, Florian Hofer, Franz Waibl, Patrick K. Quoika, Ursula Kahler, Michael Schauperl, Klaus R. Liedl
:
Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments. J. Chem. Inf. Model. 60(7): 3508-3517 (2020) - [j35]Johannes Kraml, Florian Hofer, Anna S. Kamenik
, Franz Waibl, Ursula Kahler, Michael Schauperl, Klaus R. Liedl
:
Solvation Thermodynamics in Different Solvents: Water-Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory. J. Chem. Inf. Model. 60(8): 3843-3853 (2020)
2010 – 2019
- 2019
- [j34]Lucianna Helene Santos
, Birgit J. Waldner, Julian E. Fuchs, Glaécia A. N. Pereira, Klaus R. Liedl
, Ernesto Raúl Caffarena
, Rafaela Salgado Ferreira
:
Understanding Structure-Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations. J. Chem. Inf. Model. 59(1): 137-148 (2019) - [j33]Johannes R. Loeffler
, Michael Schauperl
, Klaus R. Liedl
:
Hydration of Aromatic Heterocycles as an Adversary of π-Stacking. J. Chem. Inf. Model. 59(10): 4209-4219 (2019) - 2018
- [j32]Anna S. Kamenik
, Uta F. Lessel, Julian E. Fuchs, Thomas Fox
, Klaus R. Liedl
:
Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization. J. Chem. Inf. Model. 58(5): 982-992 (2018) - 2017
- [j31]Michael Schauperl, Paul Czodrowski
, Julian E. Fuchs, Roland G. Huber
, Birgit J. Waldner, Maren Podewitz
, Christian Kramer
, Klaus R. Liedl
:
Binding Pose Flip Explained via Enthalpic and Entropic Contributions. J. Chem. Inf. Model. 57(2): 345-354 (2017) - 2016
- [j30]Johannes R. Loeffler, Emanuel S. R. Ehmki
, Julian E. Fuchs, Klaus R. Liedl
:
Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design. J. Comput. Aided Mol. Des. 30(5): 391-400 (2016) - [j29]Birgit J. Waldner, Julian E. Fuchs, Michael Schauperl, Christian Kramer, Klaus R. Liedl
:
Protease Inhibitors in View of Peptide Substrate Databases. J. Chem. Inf. Model. 56(6): 1228-1235 (2016) - 2015
- [j28]Christian Kramer, Julian E. Fuchs, Klaus R. Liedl
:
Strong Nonadditivity as a Key Structure-Activity Relationship Feature: Distinguishing Structural Changes from Assay Artifacts. J. Chem. Inf. Model. 55(3): 483-494 (2015) - [j27]Julian E. Fuchs, Bernd Wellenzohn, Nils Weskamp
, Klaus R. Liedl
:
Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications. J. Chem. Inf. Model. 55(11): 2315-2323 (2015) - 2014
- [j26]Christian Kramer, Klaus R. Liedl
:
Limits to molecular matched-pair analysis: the experimental uncertainty case. J. Cheminformatics 6(S-1): 6 (2014) - [j25]Klaus R. Liedl
:
Entropy in specificity and thermodynamics of binding. J. Cheminformatics 6(S-1): 8 (2014) - [j24]Roland G. Huber, Michael A. Margreiter, Julian E. Fuchs, Susanne von Grafenstein, Christofer S. Tautermann
, Klaus R. Liedl
, Thomas Fox
:
Heteroaromatic π-Stacking Energy Landscapes. J. Chem. Inf. Model. 54(5): 1371-1379 (2014) - 2013
- [j23]Julian E. Fuchs, Klaus R. Liedl
:
Substrate Sequences Tell Similar Stories as Binding Cavities: Commentary. J. Chem. Inf. Model. 53(12): 3115-3116 (2013) - [j22]Christian Kramer
, Tristan Bereau
, Alexander Spinn, Klaus R. Liedl
, Peter Gedeck
, Markus Meuwly:
Deriving Static Atomic Multipoles from the Electrostatic Potential. J. Chem. Inf. Model. 53(12): 3410-3417 (2013) - [j21]Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Michael A. Margreiter, Gudrun M. Spitzer, Hannes G. Wallnoefer, Klaus R. Liedl
:
Cleavage Entropy as Quantitative Measure of Protease Specificity. PLoS Comput. Biol. 9(4) (2013) - [j20]Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Christian Kramer
, Klaus R. Liedl
:
Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos. PLoS Comput. Biol. 9(11) (2013) - 2012
- [j19]Susanne von Grafenstein, Judit Mihaly-Bison, Gerhard Wolber
, Valery N. Bochkov, Klaus R. Liedl
, Daniela Schuster
:
Identification of Novel Liver X Receptor Activators by Structure-Based Modeling. J. Chem. Inf. Model. 52(5): 1391-1400 (2012) - 2011
- [j18]Markus Muehlbacher, Gudrun M. Spitzer, Klaus R. Liedl
, Johannes Kornhuber
:
Qualitative prediction of blood-brain barrier permeability on a large and refined dataset. J. Comput. Aided Mol. Des. 25(12): 1095-1106 (2011) - [j17]Hannes G. Wallnoefer, Klaus R. Liedl
, Thomas Fox
:
A challenging system: Free energy prediction for factor Xa. J. Comput. Chem. 32(8): 1743-1752 (2011) - [j16]Hannes G. Wallnoefer, Torsten Lingott, José Gutiérrez, Irmgard Merfort, Klaus R. Liedl
:
Backbone flexibility controls the activity and specificity of a protein-protein interface - specificity in snake venom metalloproteases (SVMPs). J. Cheminformatics 3(S-1): 22 (2011) - [j15]Julian E. Fuchs, Gudrun M. Spitzer, Ameera Javed, Adam Biela, Christoph Kreutz, Bernd Wellenzohn, Klaus R. Liedl
:
Minor Groove Binders and Drugs Targeting Proteins Cover Complementary Regions in Chemical Shape Space. J. Chem. Inf. Model. 51(9): 2223-2232 (2011) - [j14]Hannes G. Wallnoefer, Klaus R. Liedl
, Thomas Fox
:
A GRID-Derived Water Network Stabilizes Molecular Dynamics Computer Simulations of a Protease. J. Chem. Inf. Model. 51(11): 2860-2867 (2011) - 2010
- [j13]Gudrun M. Spitzer, Mathias Heiss, Martina Mangold, Patrick Markt, Johannes Kirchmair
, Gerhard Wolber
, Klaus R. Liedl
:
One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space. J. Chem. Inf. Model. 50(7): 1241-1247 (2010)
2000 – 2009
- 2009
- [j12]Johannes Kirchmair
, Simona Distinto
, Patrick Markt, Daniela Schuster
, Gudrun M. Spitzer, Klaus R. Liedl
, Gerhard Wolber
:
How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information. J. Chem. Inf. Model. 49(3): 678-692 (2009) - [j11]Gudrun M. Spitzer, Bernd Wellenzohn, Patrick Markt, Johannes Kirchmair
, Thierry Langer
, Klaus R. Liedl
:
Hydrogen-Bonding Patterns of Minor Groove-Binder-DNA Complexes Reveal Criteria for Discovery of New Scaffolds. J. Chem. Inf. Model. 49(4): 1063-1069 (2009) - [j10]Monika Nocker, Sandra Handschuh, Christofer S. Tautermann
, Klaus R. Liedl
:
Theoretical Prediction of Hydrogen Bond Strength for Use in Molecular Modeling. J. Chem. Inf. Model. 49(9): 2067-2076 (2009) - 2007
- [j9]Gudrun M. Spitzer, Bernd Wellenzohn, Christian Laggner, Thierry Langer
, Klaus R. Liedl
:
DNA Minor Groove Pharmacophores Describing Sequence Specific Properties. J. Chem. Inf. Model. 47(4): 1580-1589 (2007) - 2003
- [j8]Christofer S. Tautermann
, Andreas F. Voegele, Thomas Loerting
, Peter Kaps, Klaus R. Liedl
:
Extended method for adiabatic mode reordering. J. Comput. Chem. 24(3): 386-395 (2003) - [j7]Markus J. Loferer, Hannes H. Loeffler, Klaus R. Liedl
:
A QM-MM interface between CHARMM and TURBOMOLE: Implementation and application to systems in bulk phase and biologically active systems. J. Comput. Chem. 24(10): 1240-1249 (2003) - 2001
- [j6]Hannes H. Loeffler, Christoph A. Sotriffer, Rudolf H. Winger, Klaus R. Liedl
, Bernd M. Rode:
Calculation of sequence-dependent free energies of hydration of dipeptides formed by alanine and glycine. J. Comput. Chem. 22(8): 846-860 (2001)
1990 – 1999
- 1999
- [j5]Raimundo Gargallo
, Christoph A. Sotriffer, Klaus R. Liedl
, Bernd M. Rode:
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. 13(6): 611-623 (1999) - 1998
- [j4]Somsak Tonmunphean, Sirirat Kokpol, Vudhichai Parasuk, Peter Wolschann, Rudolf H. Winger, Klaus R. Liedl
, Bernd M. Rode:
Comparative molecular field analysis of artemisinin derivatives: Ab initio versus semiempirical optimized structures. J. Comput. Aided Mol. Des. 12(4): 397-409 (1998) - 1996
- [j3]Christoph A. Sotriffer, Rudolf H. Winger, Klaus R. Liedl
, Bernd M. Rode, Janos M. Varga:
Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4. J. Comput. Aided Mol. Des. 10(4): 305-320 (1996) - [j2]Romano T. Kroemer, Peter Hecht, Klaus R. Liedl:
Different electrostatic descriptors in comparative molecular field analysis: A comparison of molecular electrostatic and coulomb potentials. J. Comput. Chem. 17(11): 1296-1308 (1996) - [j1]Teerakiat Kerdcharoen, Klaus R. Liedl, Bernd M. Rode:
Bidirectional molecular dynamics: Interpretation in terms of a modern formulation of classical mechanics. J. Comput. Chem. 17(13): 1564-1570 (1996)
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