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List of works by Klaus R. Liedl

A Cross-Reactive Human Single-Chain Antibody for Detection of Major Fish Allergens, Parvalbumins, and Identification of a Major IgE-Binding Epitope

scientific article published on 18 November 2015

A GRID-derived water network stabilizes molecular dynamics computer simulations of a protease.

scientific article

A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems

scientific article published in July 2003

A challenging system: free energy prediction for factor Xa

scientific article published on 04 March 2011

A conserved acidic residue in phenylalanine hydroxylase contributes to cofactor affinity and catalysis

scientific article

A gatekeeper helix determines the substrate specificity of Sjögren-Larsson Syndrome enzyme fatty aldehyde dehydrogenase

scientific article (publication date: 22 July 2014)

A novel paramagnetic relaxation enhancement tag for nucleic acids: a tool to study structure and dynamics of RNA.

scientific article published on 4 October 2013

About the stability of sulfurous acid (H2SO3) and its dimer

scientific article published on December 2002

Alpha-Carbonic Acid Revisited: Carbonic Acid Monomethyl Ester as a Solid and its Conformational Isomerism in the Gas Phase

scientific article published on 26 November 2019

An Unexpected Switch in Peptide Binding Mode: From Simulation to Substrate Specificity.

scientific article published on 6 December 2017

An additional substrate binding site in a bacterial phenylalanine hydroxylase

scientific article

Antibody CDR loops as ensembles in solution vs. canonical clusters from X-ray structures

scientific article published on 01 January 2020

Antipneumococcal activity of neuraminidase inhibiting artocarpin

scientific article

Antiviral potential and molecular insight into neuraminidase inhibiting diarylheptanoids from Alpinia katsumadai.

scientific article

Asymmetric arginine dimethylation of RelA provides a repressive mark to modulate TNFα/NF-κB response

scientific article published on 5 April 2016

Automated docking of ligands to antibodies: methods and applications.

scientific article

Backbone flexibility controls the activity and specificity of a protein-protein interface – specificity in snake venom metalloproteases (SVMPs).

scientific article published on 19 April 2011

Backbone flexibility controls the activity and specificity of a protein-protein interface: specificity in snake venom metalloproteases

scientific article

Balance between hydration enthalpy and entropy is important for ice binding surfaces in Antifreeze Proteins.

scientific article published on 19 September 2017

Benzimidazole inhibitors of the major cysteine protease of Trypanosoma brucei

scientific article published on 01 July 2019

Binding Pose Flip Explained via Enthalpic and Entropic Contributions.

scientific article published on 12 January 2017

Biophysical classification of a CACNA1D de novo mutation as a high-risk mutation for a severe neurodevelopmental disorder

scientific article published on 08 January 2020

Broadly neutralizing antibodies target a haemagglutinin anchor epitope

scientific article published on 23 December 2021

C5-methylation of cytosine in B-DNA thermodynamically and kinetically stabilizes BI.

scientific article

CACNA1D de novo mutations in autism spectrum disorders activate Cav1.3 L-type calcium channels

scientific article

CDR-H3 loop ensemble in solution - conformational selection upon antibody binding

scientific article published on 09 June 2019

CaB2 S4 O16 : A Borosulfate Exhibiting a New Structure Type with Phyllosilicate Analogue Topology.

scientific article published on 11 October 2017

Carbonic Acid in the Gas Phase and Its Astrophysical Relevance ⬇️

scientific article published on February 27, 1998

Carbonic acid monoethyl ester as a pure solid and its conformational isomerism in the gas-phase.

scientific article published on April 2017

Characterisation of Nox4 inhibitors from edible plants.

scientific article

Characterization of the vitamin E-binding properties of human plasma afamin

scientific article

Characterizing Protease Specificity: How Many Substrates Do We Need?

scientific article

Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties

scientific article published on 01 January 2018

Charge Anisotropy: Where Atomic Multipoles Matter Most

scientific article published on 30 September 2014

Chlorophyll Catabolites in Fall Leaves of the Wych Elm Tree Present a Novel Glycosylation Motif

scientific article published on 29 April 2016

Chlorophyll-Derived Yellow Phyllobilins of Higher Plants as Medium-Responsive Chiral Photoswitches

scientific article (publication date: 19 December 2016)

Cleavage entropy as quantitative measure of protease specificity

scientific article

Cobaltocenylidene: A Mesoionic Metalloceno Carbene, Stabilized in a Gold(III) Complex.

scientific article published on 12 January 2018

Coil-Globule Transition Thermodynamics of Poly(N-isopropylacrylamide)

scientific article published on 07 October 2019

Comparative Molecular Field Analysis of Haptens Docked to the Multispecific Antibody IgE(Lb4)

scientific article published on 01 September 1996

Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4

scientific article published on 01 August 1996

Comparative molecular field analysis of artemisinin derivatives: ab initio versus semiempirical optimized structures

scientific article published on 01 July 1998

Complementary assays helping to overcome challenges for identifying neuraminidase inhibitors

Complex of B-DNA with polyamides freezes DNA backbone flexibility

scientific article published in May 2001

Computer-guided approach to access the anti-influenza activity of licorice constituents

scientific article published on 06 December 2013

Conformational Flexibility Differentiates Naturally Occurring Bet v 1 Isoforms

scientific article published on 03 June 2017

Conformational flexibility correlates with glucose tolerance for point mutations in β-glucosidases - a computational study

scientific article published on 10 March 2020

Cooperative effects on the formation of intercalation sites

scientific article

Crystal structure of Pla l 1 reveals both structural similarity and allergenic divergence within the Ole e 1-like protein family

scientific article published on 10 December 2016

Cu[B2(SO4)4] and Cu[B(SO4)2(HSO4)] - two silicate analogue borosulfates differing in their dimensionality: a comparative study of stability and acidity

scientific article published on 23 April 2018

DNA minor groove pharmacophores describing sequence specific properties

scientific article published on 23 May 2007

DPPC-cholesterol phase diagram using coarse-grained Molecular Dynamics simulations.

scientific article

Daunomycin intercalation stabilizes distinct backbone conformations of DNA

scientific article published on 01 April 2004

Decomposing anharmonicity and mode-coupling from matrix effects in the IR spectra of matrix-isolated carbon dioxide and methane

scientific article published on 03 August 2020

Deriving static atomic multipoles from the electrostatic potential

scientific article published on 5 December 2013

Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data.

scientific article

Development of anti-viral agents using molecular modeling and virtual screening techniques

scientific article published on February 2011

Different electrostatic descriptors in comparative molecular field analysis: A comparison of molecular electrostatic and coulomb potentials

scientific article published on 01 August 1996

Discovery and Characterization of Diazenylaryl Sulfonic Acids as Inhibitors of Viral and Bacterial Neuraminidases.

scientific article published on 15 February 2017

Discovery of Retinoic Acid-Related Orphan Receptor γt Inverse Agonists via Docking and Negative Image-Based Screening

scientific article published on 11 June 2018

Dispersion dominated halogen-π interactions: energies and locations of minima.

scientific article published on 15 October 2010

Double hydrogen tunneling revisited: the breakdown of experimental tunneling criteria

scientific article published on 01 June 2004

Dynamic regulation of phenylalanine hydroxylase by simulated redox manipulation

scientific article

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

scientific article

Effects of pooling samples on the performance of classification algorithms: a comparative study

scientific article published on 30 April 2012

Elbow flexibility and ligand-induced domain rearrangements in antibody Fab NC6.8: large effects of a small hapten

scientific article published on August 2000

Electrostatic recognition in substrate binding to serine proteases.

scientific article published on 22 May 2018

Energetic and stereochemical effects of the protein environment on substrate: a theoretical study of methylmalonyl-CoA mutase

scientific article published on 01 January 2003

Enthalpic and Entropic Contributions to Hydrophobicity

scientific article published on 21 July 2016

Entropy from state probabilities: hydration entropy of cations

scientific article

Entropy in specificity and thermodynamics of binding

scientific article

Essential role of a conserved aspartate for the enzymatic activity of plasmanylethanolamine desaturase

scientific article published on 28 March 2022

Evaporation cycle experiments--a simulation of salt-induced peptide synthesis under possible prebiotic conditions

scientific article published on 01 June 1993

Exocyclic groups in the minor groove influence the backbone conformation of DNA.

scientific article

Exploring HBr ionization at the molecular level

scientific article published on 01 May 2003

Extended method for adiabatic mode reordering

scientific article published on 01 February 2003

FAH domain containing protein 1 (FAHD-1) is required for mitochondrial function and locomotion activity in C. elegans

scientific article (publication date: 2015)

Fold stability during endolysosomal acidification is a key factor for allergenicity and immunogenicity of the major birch pollen allergen

scientific article (publication date: May 2016)

Gaining in pan-affinity towards sigma 1 and sigma 2 receptors. SAR studies on arylalkylamines.

scientific article published on 11 October 2016

Helix morphology changes in B-DNA induced by spontaneous B(I)<==>B(II) substrate interconversion

scientific article published on 01 October 1999

Heteroaromatic π-stacking energy landscapes.

scientific article published on 9 May 2014

Heteroligation of a mouse monoclonal IgE antibody (La2) with small molecules, analysed by computer-aided automated docking

scientific article published on 01 February 1996

High-Pressure Synthesis and Characterization of the Ammonium Yttrium Borate (NH4)YB8O14.

scientific article published in November 2017

High-Pressure Synthesis of Cd(NH₃)₂[B₃O₅(NH₃)]₂: Pioneering the Way to the Substance Class of Ammine Borates

scientific article published on 27 April 2015

Highly Electrophilic, Catalytically Active and Redox-Responsive Cobaltoceniumyl and Ferrocenyl Triazolylidene Coinage Metal Complexes.

scientific article

How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information

scientific article published on 01 March 2009

Hydration of Aromatic Heterocycles as an Adversary of π-Stacking

scientific article published on 17 October 2019

Hydration of hydroxypyrrole influences binding of ImHpPyPy-beta-Dp polyamide to DNA.

scientific article

Hydration thermodynamics of cytosolic phospholipase A2 GIVA predict its membrane-associated parts and its highly hydrated binding site

scientific article published on 14 March 2020

Hydrogen-bonding patterns of minor groove-binder-DNA complexes reveal criteria for discovery of new scaffolds

scientific article

Identification of FAH domain-containing protein 1 (FAHD1) as oxaloacetate decarboxylase

scientific article

Identification of PPARgamma partial agonists of natural origin (I): development of a virtual screening procedure and in vitro validation

scientific article

Identification of dual Sigma1 receptor modulators/acetylcholinesterase inhibitors with antioxidant and neurotrophic properties, as neuroprotective agents

scientific article published on 08 September 2018

Identification of novel functional inhibitors of acid sphingomyelinase

scientific article published in 2011

Identification of novel liver X receptor activators by structure-based modeling

scientific article

Implementation of the Freely Jointed Chain Model to Assess Kinetics and Thermodynamics of Thermosensitive Coil-Globule Transition by Markov States

scientific article published on 04 May 2021

Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding

scientific article published on 24 February 2015

Indirect readout of the trp-repressor-operator complex by B-DNA's backbone conformation transitions

scientific article published in March 2002

Influence of backbone conformations of human carbonic anhydrase II on carbon dioxide hydration: hydration pathways and binding of bicarbonate.

scientific article

Influence of netropsin's charges on the minor groove width of d(CGCGAATTCGCG)2.

scientific article

Influenza neuraminidase: a druggable target for natural products

scientific article published on 25 October 2011

Interface dynamics explain assembly dependency of influenza neuraminidase catalytic activity.

scientific article

Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design

scientific article

Ligand binding by antibody IgE Lb4: assessment of binding site preferences using microcalorimetry, docking, and free energy simulations.

scientific article

Ligand binding modulates the structural dynamics and compactness of the major birch pollen allergen.

scientific article published on December 2014

Ligand-induced domain movement in an antibody Fab: molecular dynamics studies confirm the unique domain movement observed experimentally for Fab NC6.8 upon complexation and reveal its segmental flexibility

scientific article published on 01 May 1998

Limits to molecular matched-pair analysis: the experimental uncertainty case

scientific article

Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD.

scientific article published on 20 June 2016

M.TaqI facilitates the base flipping via an unusual DNA backbone conformation

scientific article published in October 2005

Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications

scientific article

Matched molecular pair analysis: significance and the impact of experimental uncertainty

scientific article published on 16 April 2014

Matrix isolation studies of carbonic acid--the vapor phase above the β-polymorph.

scientific article published on 14 May 2013

Mechanism of Olefin Metathesis with Neutral and Cationic Molybdenum Imido Alkylidene N-Heterocyclic Carbene Complexes

scientific article published on 09 May 2019

Mechanisms Responsible for ω-Pore Currents in Cav Calcium Channel Voltage-Sensing Domains.

scientific article published in October 2017

Minor groove binders and drugs targeting proteins cover complementary regions in chemical shape space

scientific article published on 26 August 2011

Modeling anhydrous and aqua copper(II) amino acid complexes: a new molecular mechanics force field parametrization based on quantum chemical studies and experimental crystal data.

scientific article

Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases

scientific article published on 04 September 2019

Molecular docking studies of natural cholinesterase-inhibiting steroidal alkaloids from Sarcococca saligna

scientific article published in November 2003

Molecular dynamics simulation studies of novel β-lactamase inhibitor.

scientific article published on 04 April 2017

N-Heterocyclic Carbene Gold(I) Complexes: Mechanism of the Ligand Scrambling Reaction and Their Oxidation to Gold(III) in Aqueous Solutions

scientific article published on 02 October 2020

New High-Pressure Gallium Borate Ga2B3O7(OH) with Photocatalytic Activity.

scientific article published on 24 December 2015

Non-(13)CO2 targeted breath tests: a feasibility study

scientific article published on 30 October 2014

Novel Types of Hypermodified Fluorescent Phyllobilins from Breakdown of Chlorophyll in Senescent Leaves of Grapevine (Vitis vinifera)

scientific article published on 22 November 2018

Novel neuraminidase inhibitors: identification, biological evaluation and investigations of the binding mode

scientific article

One concept, three implementations of 3D pharmacophore-based virtual screening: distinct coverage of chemical search space

scientific article published in July 2010

Pathogenicity of de novo CACNA1D Ca2+ channel variants predicted from sequence co-variation

scientific article published in 2024

Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization.

scientific article

Polarizable and non-polarizable force fields: Protein folding, unfolding, and misfolding

scientific article published on 01 November 2020

Polyreactive Broadly Neutralizing B cells Are Selected to Provide Defense against Pandemic Threat Influenza Viruses

scientific article published on 17 October 2020

Porphyrin-LEGO®: synthesis of a hexafullereno-diporphyrin using porphyrins programmed for [4+2]-cycloaddition

scientific article published on 26 March 2012

Precursors for cytochrome P450 profiling breath tests from an in silico screening approach

scientific article published on 18 September 2014

Prediction of IgE(Lb4)-ligand complex structures by automated docking

scientific article published in May 1996

Prediction of blood:air and fat:air partition coefficients of volatile organic compounds for the interpretation of data in breath gas analysis

scientific article

Prediction of the structure of human Janus kinase 2 (JAK2) comprising the two carboxy-terminal domains reveals a mechanism for autoregulation

scientific article published in January 2001

Profiling selectivity of chagasin mutants towards cysteine proteases cruzain or cathepsin L through molecular dynamics simulations

scientific article published on 25 July 2020

Protease Inhibitors in View of Peptide Substrate Databases

scientific article published on June 2016

PvuII-endonuclease induces structural alterations at the scissile phosphate group of its cognate DNA.

scientific article

Pyro-Phyllobilins - Elusive Chlorophyll Catabolites Lacking a Critical Carboxylate Function of the Natural Chlorophylls

scientific article published on 31 January 2018

Qualitative prediction of blood-brain barrier permeability on a large and refined dataset

scientific article

Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases

scientific article published on 28 December 2015

Quantitative analysis of the structural requirements for blockade of the N-methyl-D-aspartate receptor at the phencyclidine binding site

scientific article published in January 1998

Raman spectroscopic study of the phase transition of amorphous to crystalline beta-carbonic acid

scientific article published on January 2009

Reciprocal regulation of PKA and Rac signaling ⬇️

scientific article published on May 8, 2013

STACKED - Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding

scientific article published on 19 March 2020

Sequence diversity of NanA manifests in distinct enzyme kinetics and inhibitor susceptibility

scientific article

Sequence-specific positions of water molecules at the interface between DNA and minor groove binders

scientific article

Sodium-induced population shift drives activation of thrombin

scientific article published on 23 January 2020

Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces

scientific article published on 24 October 2019

Specificity of a protein-protein interface: local dynamics direct substrate recognition of effector caspases

scientific article published on 19 October 2013

Specificity of a protein–protein interface: Local dynamics direct substrate recognition of effector caspases

scientific article published on 24 September 2014

Spectroscopic observation of matrix-isolated carbonic acid trapped from the gas phase

scientific article published on 22 December 2010

Stabilizing of a globular protein by a highly complex water network: a molecular dynamics simulation study on factor Xa.

scientific article published in June 2010

Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA.

scientific article

Strong nonadditivity as a key structure-activity relationship feature: distinguishing structural changes from assay artifacts

scientific article

Structural Basis of the Immunological Cross-Reactivity between Kiwi and Birch Pollen

scientific article published in 2023

Structural basis for the bi-functionality of human oxaloacetate decarboxylase FAHD1

article

Structure of the Major Apple Allergen Mal d 1

scientific article published on 5 February 2017

Substrate sequences tell similar stories as binding cavities: commentary

scientific article published on December 2013

Substrate-driven mapping of the degradome by comparison of sequence logos

scientific article (publication date: 2013)

The Hydrogenobyric Acid Structure Reveals the Corrin Ligand as an Entatic State Module Empowering B12 Cofactors for Catalysis

scientific article published on 26 June 2019

The N6-methyl group of adenine further increases the BI stability of DNA compared to C5-methyl groups

scientific article published on 01 January 2005

The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery

scientific article

The conformer substates of nonoriented B-type DNA in double helical poly(dG-dC)

scientific article published on 01 February 2003

The flexibility of the protein neuraminidase opens new possibilities for drug development

scientific article

The fumarylacetoacetate hydrolase (FAH) superfamily of enzymes: multifunctional enzymes from microbes to mitochondria.

scientific article published on 27 February 2018

The ground-state tunneling splitting of various carboxylic acid dimers.

scientific article

The impact of nitration on the structure and immunogenicity of the major birch pollen allergen Bet v 1.0101.

scientific article

The intermolecular anthracene-transfer in a regiospecific antipodal C60 difunctionalization

scientific article published on 19 May 2020

The reaction rate constant of chlorine nitrate hydrolysis

scientific article published on 01 April 2001

Theoretical prediction of hydrogen bond strength for use in molecular modeling

scientific article published in September 2009

Thermosensitive Hydration of Four Acrylamide-Based Polymers in Coil and Globule Conformations

scientific article published on 15 October 2020

Toward Elimination of Discrepancies between Theory and Experiment: Anharmonic Rotational-Vibrational Spectrum of Water in Solid Noble Gas Matrices

scientific article published on 12 September 2019

Toward elimination of discrepancies between theory and experiment: the rate constant of the atmospheric conversion of SO3 to H2SO4.

scientific article

Toward novel inhibitors against KdsB: a highly specific and selective broad-spectrum bacterial enzyme.

scientific article published on 31 March 2018

Towards an understanding of DNA recognition by the methyl-CpG binding domain 1.

scientific article

Towards the experimental decomposition rate of carbonic acid (H2CO3) in aqueous solution

scientific article published in January 2002

Transitions of CDR-L3 Loop Canonical Cluster Conformations on the Micro-to-Millisecond Timescale

scientific article published on 19 November 2019

Understanding Structure-Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations

scientific article published on 21 December 2018

Unexpected BII conformer substate population in unoriented hydrated films of the d(CGCGAATTCGCG)2 dodecamer and of native B-DNA from salmon testes

scientific article published on July 1999

Unique macrocycles in the Taiwan traditional Chinese medicine database

scientific article published on 9 April 2015

VH -VL interdomain dynamics observed by computer simulations and NMR

scientific article published on 06 January 2020

Water-mediated contacts in the trp-repressor operator complex recognition process

scientific article published in April 2004

Why Are Copper(II) Amino Acid Complexes Not Planar in Their Crystal Structures? An ab Initio and Molecular Mechanics Study

scientific article published on 01 June 1999

Z-DNA's conformer substates revealed by FT-IR difference spectroscopy of nonoriented left-handed double helical poly(dG-dC)

scientific article published on 01 April 2005

Zinc Substitution of Cobalt in Vitamin B12 : Zincobyric acid and Zincobalamin as Luminescent Structural B12 -Mimics

scientific article published on 04 September 2019

pH-Dependent Protonation of the Phl p 6 Pollen Allergen Studied by NMR and cpH-aMD

scientific article published on 12 September 2019

pyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules

scientific article published in 2021

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