List of works - Holger Gohlke

A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins

scientific article published on 23 June 2011

AMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools

scientific article published on 01 June 2020

Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM.

scientific article

Alignment-Independent Comparison of Binding Sites Based on DrugScore Potential Fields Encoded by 3D Zernike Descriptors ⬇️

scientific article published on August 22, 2012

Alkoxyurea-Based Histone Deacetylase Inhibitors Increase Cisplatin Potency in Chemoresistant Cancer Cell Lines

scientific article

Automated and optimally FRET-assisted structural modeling

scientific article published on 26 October 2020

Basal Histamine H4 Receptor Activation: Agonist Mimicry by the Diphenylalanine Motif

scientific article published on 16 October 2019

Binding modes of thioflavin T and Congo red to the fibril structure of amyloid-β(1-42)

scientific article published on 08 June 2020

Binding region of alanopine dehydrogenase predicted by unbiased molecular dynamics simulations of ligand diffusion

scientific article published on 25 September 2013

Characterization of the nucleotide-binding domain NsrF from the BceAB-type ABC-transporter NsrFP from the human pathogen Streptococcus agalactiae

scientific article published on 16 September 2020

Chlorflavonin Targets Acetohydroxyacid Synthase Catalytic Subunit IlvB1 for Synergistic Killing of Mycobacterium tuberculosis

scientific article

Co-culture of the fungus Fusarium tricinctum with Streptomyces lividans induces production of cryptic naphthoquinone dimers

scientific article published on 11 January 2019

Consensus adaptation of fields for molecular comparison (AFMoC) models incorporate ligand and receptor conformational variability into tailor-made scoring functions

scientific article published on 25 October 2007

Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function

scientific article

Converging a Knowledge-Based Scoring Function: DrugScore2018

scientific article published on 18 December 2018

Corrigendum to: Posttranslational Modification of the NADP-Malic Enzyme Involved in C4 Photosynthesis Modulates the Enzymatic Activity during the Day

scientific article published on 24 October 2021

Cosolvent-Enhanced Sampling and Unbiased Identification of Cryptic Pockets Suitable for Structure-Based Drug Design

scientific article published on 06 May 2019

Design, Multicomponent Synthesis, and Anticancer Activity of a Focused Histone Deacetylase (HDAC) Inhibitor Library with Peptoid-Based Cap Groups

scientific article

Design, synthesis and biological evaluation of β-peptoid-capped HDAC inhibitors with anti-neuroblastoma and anti-glioblastoma activity

scientific article published on 23 October 2018

Dimerization energetics of the G-protein coupled bile acid receptor TGR5 from all-atom simulations

scientific article published on 27 December 2019

DrugScoreRNA--knowledge-based scoring function to predict RNA-ligand interactions

scientific article

EDTA aggregates induce SYPRO orange-based fluorescence in thermal shift assay

scientific article

Effects of novel HDAC inhibitors on urothelial carcinoma cells.

scientific article published on 31 July 2018

Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations

scientific article published on 20 December 2016

Ensemble- and Rigidity Theory-Based Perturbation Approach To Analyze Dynamic Allostery

scientific article published on 7 November 2017

Evidence for functional selectivity in TUDC- and norUDCA-induced signal transduction via α5β1 integrin towards choleresis

scientific article published on 02 April 2020

Foamy Viruses, Bet, and APOBEC3 Restriction

scientific article published in 2021

From determinants of RUNX1/ETO tetramerization to small-molecule protein-protein interaction inhibitors targeting acute myeloid leukemia

scientific article

HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations ⬇️

scientific article published on August 23, 2010

Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein–Protein Interface ⬇️

scientific article published on December 27, 2011

How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces?

scientific article published on 30 October 2012

Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy - entropy compensation

scientific article published in Scientific Reports

Interdependence of a mechanosensitive anion channel and glutamate receptors in distal wound signaling

scientific article published on 08 September 2021

Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations

scientific article

Isoform-specific Inhibition of N-methyl-D-aspartate Receptors by Bile Salts

scientific article published on 11 July 2019

Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.

scientific article

N 6-modified cAMP derivatives that activate protein kinase A also act as full agonists of murine HCN2 channels

scientific article published on 15 October 2019

Nutrient exchange in arbuscular mycorrhizal symbiosis from a thermodynamic point of view

scientific article published on 21 January 2019

On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation

scientific article published on 10 April 2018

On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase.

scientific article published on 14 August 2017

PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building

scientific article published on 12 June 2019

Partially inserted nascent chain unzips the lateral gate of the Sec translocon

scientific article published on 05 August 2019

Phosphorylated tyrosine 93 of hepatitis C virus nonstructural protein 5A is essential for interaction with host c-Src and efficient viral replication

scientific article published on 12 March 2019

Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins ⬇️

scientific article published on September 30, 2011

Posttranslational Modification of the NADP-Malic Enzyme Involved in C4 Photosynthesis Modulates the Enzymatic Activity during the Day

scientific article published on 30 July 2019

Quality matters: extension of clusters of residues with good hydrophobic contacts stabilize (hyper)thermophilic proteins

scientific article published on 28 January 2014

Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins

scientific article published on 07 April 2020

Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1.

scientific article published in March 2018

Recurrent Germline Variant in RAD21 Predisposes Children to Lymphoblastic Leukemia or Lymphoma

scientific article published on 05 May 2022

Resolving dynamics and function of transient states in single enzyme molecules

scientific article published on 06 March 2020

Steering protein-ligand docking with quantitative NMR chemical shift perturbations

scientific article published in October 2009

Structural, mechanistic, and physiological insights into phospholipase A-mediated membrane phospholipid degradation in Pseudomonas aeruginosa

scientific article published on 10 May 2022

Structure and efflux mechanism of the yeast pleiotropic drug resistance transporter Pdr5

scientific article published on 06 September 2021

Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity

scientific article published in 2021

Surprising Non-Additivity of Methyl Groups in Drug-Kinase Interaction

scientific article published on 04 November 2019

Synthesis of Peptoid-Based Class I-Selective Histone Deacetylase Inhibitors with Chemosensitizing Properties

scientific article published on 17 December 2019

Systematic analysis of ATG13 domain requirements for autophagy induction.

scientific article published on 26 November 2017

Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A

scientific article published on 16 January 2020

Targeting HSP90 dimerization via the C terminus is effective in imatinib-resistant CML and lacks the heat shock response

scientific article published on 03 May 2018

Tertiary Interactions in the Unbound Guanine-Sensing Riboswitch Focus Functional Conformational Variability on the Binding Site.

scientific article published on 11 October 2017

The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A

scientific article published on 16 October 2019

TopDomain: Exhaustive Protein Domain Boundary Metaprediction Combining Multisource Information and Deep Learning

scientific article published on 23 June 2021

TopModel: Template-Based Protein Structure Prediction at Low Sequence Identity Using Top-Down Consensus and Deep Neural Networks

scientific article published on 06 February 2020

TopProperty: Robust Metaprediction of Transmembrane and Globular Protein Features Using Deep Neural Networks

scientific article published on 20 October 2021

TopScore: Using Deep Neural Networks and Large Diverse Data Sets for Accurate Protein Model Quality Assessment

scientific article published on 09 October 2018

Understanding the inhibitory effect of highly potent and selective archazolides binding to the vacuolar ATPase

scientific article

α-Aminoxy Peptoids: A Unique Peptoid Backbone with a Preference for cis-Amide Bonds.

scientific article published on 16 January 2017

List of works by Holger Gohlke

A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins

AMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools

Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM.

Alignment-Independent Comparison of Binding Sites Based on DrugScore Potential Fields Encoded by 3D Zernike Descriptors ⬇️

Alkoxyurea-Based Histone Deacetylase Inhibitors Increase Cisplatin Potency in Chemoresistant Cancer Cell Lines

Automated and optimally FRET-assisted structural modeling

Basal Histamine H4 Receptor Activation: Agonist Mimicry by the Diphenylalanine Motif

Binding modes of thioflavin T and Congo red to the fibril structure of amyloid-β(1-42)

Binding region of alanopine dehydrogenase predicted by unbiased molecular dynamics simulations of ligand diffusion

Characterization of the nucleotide-binding domain NsrF from the BceAB-type ABC-transporter NsrFP from the human pathogen Streptococcus agalactiae

Chlorflavonin Targets Acetohydroxyacid Synthase Catalytic Subunit IlvB1 for Synergistic Killing of Mycobacterium tuberculosis

Co-culture of the fungus <i>Fusarium tricinctum</i> with <i>Streptomyces lividans</i> induces production of cryptic naphthoquinone dimers

Consensus adaptation of fields for molecular comparison (AFMoC) models incorporate ligand and receptor conformational variability into tailor-made scoring functions

Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function

Converging a Knowledge-Based Scoring Function: DrugScore2018

Corrigendum to: Posttranslational Modification of the NADP-Malic Enzyme Involved in C4 Photosynthesis Modulates the Enzymatic Activity during the Day

Cosolvent-Enhanced Sampling and Unbiased Identification of Cryptic Pockets Suitable for Structure-Based Drug Design

Design, Multicomponent Synthesis, and Anticancer Activity of a Focused Histone Deacetylase (HDAC) Inhibitor Library with Peptoid-Based Cap Groups

Design, synthesis and biological evaluation of β-peptoid-capped HDAC inhibitors with anti-neuroblastoma and anti-glioblastoma activity

Dimerization energetics of the G-protein coupled bile acid receptor TGR5 from all-atom simulations

DrugScoreRNA--knowledge-based scoring function to predict RNA-ligand interactions

EDTA aggregates induce SYPRO orange-based fluorescence in thermal shift assay

Effects of novel HDAC inhibitors on urothelial carcinoma cells.

Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations

Ensemble- and Rigidity Theory-Based Perturbation Approach To Analyze Dynamic Allostery

Evidence for functional selectivity in TUDC- and norUDCA-induced signal transduction via α5β1 integrin towards choleresis

Foamy Viruses, Bet, and APOBEC3 Restriction

From determinants of RUNX1/ETO tetramerization to small-molecule protein-protein interaction inhibitors targeting acute myeloid leukemia

HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations ⬇️

Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein–Protein Interface ⬇️

How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces?

Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy - entropy compensation

Interdependence of a mechanosensitive anion channel and glutamate receptors in distal wound signaling

Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations

Isoform-specific Inhibition of N-methyl-D-aspartate Receptors by Bile Salts

Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.

N 6-modified cAMP derivatives that activate protein kinase A also act as full agonists of murine HCN2 channels

Nutrient exchange in arbuscular mycorrhizal symbiosis from a thermodynamic point of view

On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation

On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase.

PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building

Partially inserted nascent chain unzips the lateral gate of the Sec translocon

Phosphorylated tyrosine 93 of hepatitis C virus nonstructural protein 5A is essential for interaction with host c-Src and efficient viral replication

Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins ⬇️

Posttranslational Modification of the NADP-Malic Enzyme Involved in C4 Photosynthesis Modulates the Enzymatic Activity during the Day

Quality matters: extension of clusters of residues with good hydrophobic contacts stabilize (hyper)thermophilic proteins

Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins

Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1.

Recurrent Germline Variant in <i>RAD21</i> Predisposes Children to Lymphoblastic Leukemia or Lymphoma

Resolving dynamics and function of transient states in single enzyme molecules

Steering protein-ligand docking with quantitative NMR chemical shift perturbations

Structural, mechanistic, and physiological insights into phospholipase A-mediated membrane phospholipid degradation in <i>Pseudomonas aeruginosa</i>

Structure and efflux mechanism of the yeast pleiotropic drug resistance transporter Pdr5

Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity

Surprising Non-Additivity of Methyl Groups in Drug-Kinase Interaction

Synthesis of Peptoid-Based Class I-Selective Histone Deacetylase Inhibitors with Chemosensitizing Properties

Systematic analysis of ATG13 domain requirements for autophagy induction.

Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A

Targeting HSP90 dimerization via the C terminus is effective in imatinib-resistant CML and lacks the heat shock response

Tertiary Interactions in the Unbound Guanine-Sensing Riboswitch Focus Functional Conformational Variability on the Binding Site.

The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A

TopDomain: Exhaustive Protein Domain Boundary Metaprediction Combining Multisource Information and Deep Learning

TopModel: Template-Based Protein Structure Prediction at Low Sequence Identity Using Top-Down Consensus and Deep Neural Networks

TopProperty: Robust Metaprediction of Transmembrane and Globular Protein Features Using Deep Neural Networks

TopScore: Using Deep Neural Networks and Large Diverse Data Sets for Accurate Protein Model Quality Assessment

Understanding the inhibitory effect of highly potent and selective archazolides binding to the vacuolar ATPase

α-Aminoxy Peptoids: A Unique Peptoid Backbone with a Preference for cis-Amide Bonds.