List of works - Johannes Kirchmair

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

scientific article (publication date: April 2016)

A mini-review of the anti-SARS-CoV-2 potency of Amaryllidaceae alkaloids

scientific article published in July 2024

ALADDIN: Docking Approach Augmented by Machine Learning for Protein Structure Selection Yields Superior Virtual Screening Performance

scientific article published on 08 November 2019

Alignment-Based Prediction of Sites of Metabolism.

scientific article published on 18 May 2017

Analysis of the FLVR motif of SHIP1 and its importance for the protein stability of SH2 containing signaling proteins

scientific article published on 01 August 2019

Anti-cancer drug development: computational strategies to identify and target proteins involved in cancer metabolism

scientific article published on January 2013

Antipneumococcal activity of neuraminidase inhibiting artocarpin

scientific article

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

scientific article

Applications of integrated data mining methods to exploring natural product space for acetylcholinesterase inhibitors ⬇️

scientific article

Aryl Bis-Sulfonamide Inhibitors of IspF fromArabidopsis thalianaandPlasmodium falciparum

scholarly article by Jonas Thelemann et al published 5 October 2015 in ChemMedChem

Azepine-Indole Alkaloids From Psychotria nemorosa Modulate 5-HT2A Receptors and Prevent in vivo Protein Toxicity in Transgenic Caenorhabditis elegans

scientific article published in 2022

Barbituric acid derivative BAS 02104951 inhibits PKCε, PKCη, PKCε/RACK2 interaction, Elk-1 phosphorylation in HeLa and PKCε and η translocation in PC3 cells following TPA-induction

scientific article published on 24 December 2010

Benchmarking Commercial Conformer Ensemble Generators

scientific article

BonMOLière: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein Space ⬇️

journal article from 'International Journal of Molecular Sciences' published in 2021

CAESAR: a new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration

scientific article published on 11 August 2007

Chapter 3. Pharmacophore-based Virtual Screening in Drug Discovery

Characterization of the Chemical Space of Known and Readily Obtainable Natural Products

scientific article published on 01 August 2018

ChemBioSim: Enhancing Conformal Prediction of In Vivo Toxicity by Use of Predicted Bioactivities

publication published on 21 June 2021

Cheminformatics in Natural Product-Based Drug Discovery

scientific article published on 28 July 2020

Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms

scientific article published in March 2005

Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations

scientific article published in July 2006

Complementary assays helping to overcome challenges for identifying neuraminidase inhibitors

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

scientific article

Computational approaches for skin sensitization prediction

scientific article published on 01 October 2018

Computational methods and tools to predict cytochrome P450 metabolism for drug discovery

scientific article published on 15 January 2019

Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms

scientific article (publication date: 26 March 2012)

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

scientific article published on 06 December 2013

Conformator: A Novel Method for the Generation of Conformer Ensembles

scientific article published on 12 February 2019

Critical comparison of virtual screening methods against the MUV data set.

scientific article

Cryo-EM structure of pleconaril-resistant rhinovirus-B5 complexed to the antiviral OBR-5-340 reveals unexpected binding site

scientific article published on 28 August 2019

Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers

scientific article (publication date: 2014)

Data Resources for the Computer-Guided Discovery of Bioactive Natural Products

scientific article published on 30 August 2017

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

scientific article published on February 2011

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

scientific article published on 15 February 2017

Discovery of Bioactive Natural Products for the Treatment of Acute Respiratory Infections - An Integrated Approach.

scientific article published on 19 March 2018

Discovery of Novel Natural Neuraminidase Inhibitors (NAI) based on In Silico Screening and Antiviral Investigations

article published in 2011

Discovery of nonsteroidal 17beta-hydroxysteroid dehydrogenase 1 inhibitors by pharmacophore-based screening of virtual compound libraries

scientific article

Discovery of novel CB2 receptor ligands by a pharmacophore-based virtual screening workflow

scientific article published in January 2009

Discovery of novel PPAR ligands by a virtual screening approach based on pharmacophore modeling, 3D shape, and electrostatic similarity screening

scientific article published on 27 September 2008

Discovery of novel cathepsin S inhibitors by pharmacophore-based virtual high-throughput screening

scientific article published on 19 July 2008

Discovery of prenylated flavonoids with dual activity against influenza virus and Streptococcus pneumoniae

scientific article published on 3 June 2016

Disruption of the viral polymerase complex assembly as a novel approach to attenuate influenza A virus

scientific article

Dual Acting Neuraminidase Inhibitors Open New Opportunities to Disrupt the Lethal Synergism between Streptococcus pneumoniae and Influenza Virus.

scientific article

Enhancing drug discovery through in silico screening: strategies to increase true positives retrieval rates.

scientific article published on January 2008

Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection--what can we learn from earlier mistakes?

scientific article published on 15 January 2008

FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity

scientific article

FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes

scientific article published on 30 July 2019

FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes

scientific article published on 12 November 2013

Fast and efficient in silico 3D screening: toward maximum computational efficiency of pharmacophore-based and shape-based approaches

scientific article published on 11 October 2007

From in silico target prediction to multi-target drug design: current databases, methods and applications

scientific article

GLORY: Generator of the Structures of Likely Cytochrome P450 Metabolites Based on Predicted Sites of Metabolism

scientific article published on 12 June 2019

GLORYx: Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics

scientific article published on 10 August 2020

HDAC3i-Finder: A Machine Learning-based Computational Tool to Screen for HDAC3 Inhibitors

scientific article published on 16 October 2020

High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators

scientific article published on 16 February 2017

Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters

article

Hit Dexter: A Machine-learning Model for the Prediction of Frequent Hitters.

scientific article published on 29 December 2017

How Diverse Are the Protein-Bound Conformations of Small-Molecule Drugs and Cofactors?

scientific article published on 27 March 2018

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

scientific article published on 01 March 2009

How do metabolites differ from their parent molecules and how are they excreted?

scientific article

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

scientific article

INH14, a Small-Molecule Urea Derivative, Inhibits the IKKα/β-Dependent TLR Inflammatory Response

scientific article published on 29 January 2019

Identification of HIV-1 Reverse Transcriptase Dual Inhibitors by a Combined Shape-, 2D-Fingerprint- and Pharmacophore-based Virtual Screening Approach

article

Identification of HIV-1 reverse transcriptase dual inhibitors by a combined shape-, 2D-fingerprint- and pharmacophore-based virtual screening approach

scientific article

Identification of chemically diverse, novel inhibitors of 17β-hydroxysteroid dehydrogenase type 3 and 5 by pharmacophore-based virtual screening

scientific article published on 12 February 2011

In Silico Models to Predict the Perturbation of Molecular Initiating Events Related to Thyroid Hormone Homeostasis

scientific article published on 13 November 2020

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

Modulators of Protein-Protein Interactions – Novel Approaches in Targeting Protein Kinases and Other Pharmaceutically Relevant Biomolecules ⬇️

scientific article published on January 1, 2011

Molecular mechanism of a specific capsid binder resistance caused by mutations outside the binding pocket

scientific article

Morphinans and isoquinolines: acetylcholinesterase inhibition, pharmacophore modeling, and interaction with opioid receptors.

scientific article

N-thiadiazole-4-hydroxy-2-quinolone-3-carboxamides bearing heteroaromatic rings as novel antibacterial agents: Design, synthesis, biological evaluation and target identification

scientific article published on 30 December 2019

NERDD: a web portal providing access to in silico tools for drug discovery

scientific article published on 01 February 2020

NP-Scout: Machine Learning Approach for the Quantification and Visualization of the Natural Product-Likeness of Small Molecules

scientific article published on 24 January 2019

Natural products against acute respiratory infections: Strategies and lessons learned

scientific article published on 11 October 2019

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

scientific article

Novel pharmacological chaperones that correct phenylketonuria in mice.

scientific article

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

scientific article published in July 2010

PAIN(S) relievers for medicinal chemists: how computational methods can assist in hit evaluation

scientific article published on 29 June 2018

Pharmacophore modeling and parallel screening for PPAR ligands

article

Platform for determining the inhibition profile of neuraminidase inhibitors in an influenza virus N1 background

scientific article

Predicting Cyclooxygenase Inhibition by Three-Dimensional Pharmacophoric Profiling. Part I: Model Generation, Validation and Applicability in Ethnopharmacology

scientific article

Predicting drug metabolism: experiment and/or computation?

scientific article published on 24 April 2015

Pyrazolopyrimidines: Potent Inhibitors Targeting the Capsid of Rhino- and Enteroviruses

scientific article

Quantifying the shifts in physicochemical property space introduced by the metabolism of small organic molecules.

scientific article published on 22 March 2013

Rationality over fashion and hype in drug design

scientific article published on 18 May 2021

Resources for Chemical, Biological, and Structural Data on Natural Products

scientific article published on 01 January 2019

Ring systems in natural products: structural diversity, physicochemical properties, and coverage by synthetic compounds

scientific article published in January 2022

Scope of 3D Shape-Based Approaches in Predicting the Macromolecular Targets of Structurally Complex Small Molecules Including Natural Products and Macrocyclic Ligands

scientific article published on 05 May 2020

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

scientific article

Similarity-Based Methods and Machine Learning Approaches for Target Prediction in Early Drug Discovery: Performance and Scope ⬇️

journal article from 'International Journal of Molecular Sciences' published in 2020

Skin Doctor CP: Conformal Prediction of the Skin Sensitization Potential of Small Organic Molecules

scientific article published on 09 December 2020

Skin Doctor: Machine Learning Models for Skin Sensitization Prediction that Provide Estimates and Indicators of Prediction Reliability

scientific article published on 28 September 2019

Structure-based virtual screening for the discovery of natural inhibitors for human rhinovirus coat protein

scientific article published on 5 February 2008

Support Vector Machine (SVM) Models for Predicting Inhibitors of the 3' Processing Step of HIV-1 Integrase

scientific article published on 9 September 2013

Synthesis and biological assessment of novel 2-thiazolylhydrazones and computational analysis of their recognition by monoamine oxidase B.

scientific article

Synthesis, semipreparative HPLC separation, biological evaluation, and 3D-QSAR of hydrazothiazole derivatives as human monoamine oxidase B inhibitors

scientific article published in June 2010

Tackling Antimicrobial Resistance with Small Molecules Targeting LsrK: Challenges and Opportunities

scientific article published on 05 November 2020

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

scientific article

The challenges involved in modeling toxicity data in silico: a review

scientific article

Thienoquinolines as novel disruptors of the PKCε/RACK2 protein-protein interaction

scientific article published on 08 April 2014

List of works by Johannes Kirchmair

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

A mini-review of the anti-SARS-CoV-2 potency of Amaryllidaceae alkaloids

ALADDIN: Docking Approach Augmented by Machine Learning for Protein Structure Selection Yields Superior Virtual Screening Performance

Alignment-Based Prediction of Sites of Metabolism.

Analysis of the FLVR motif of SHIP1 and its importance for the protein stability of SH2 containing signaling proteins

Anti-cancer drug development: computational strategies to identify and target proteins involved in cancer metabolism

Antipneumococcal activity of neuraminidase inhibiting artocarpin

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

Applications of integrated data mining methods to exploring natural product space for acetylcholinesterase inhibitors ⬇️

Aryl Bis-Sulfonamide Inhibitors of IspF fromArabidopsis thalianaandPlasmodium falciparum

Azepine-Indole Alkaloids From Psychotria nemorosa Modulate 5-HT2A Receptors and Prevent in vivo Protein Toxicity in Transgenic Caenorhabditis elegans

Barbituric acid derivative BAS 02104951 inhibits PKCε, PKCη, PKCε/RACK2 interaction, Elk-1 phosphorylation in HeLa and PKCε and η translocation in PC3 cells following TPA-induction

Benchmarking Commercial Conformer Ensemble Generators

BonMOLière: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein Space ⬇️

CAESAR: a new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration

Chapter 3. Pharmacophore-based Virtual Screening in Drug Discovery

Characterization of the Chemical Space of Known and Readily Obtainable Natural Products

ChemBioSim: Enhancing Conformal Prediction of In Vivo Toxicity by Use of Predicted Bioactivities

Cheminformatics in Natural Product-Based Drug Discovery

Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms

Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations

Complementary assays helping to overcome challenges for identifying neuraminidase inhibitors

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

Computational approaches for skin sensitization prediction

Computational methods and tools to predict cytochrome P450 metabolism for drug discovery

Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms

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

Conformator: A Novel Method for the Generation of Conformer Ensembles

Critical comparison of virtual screening methods against the MUV data set.

Cryo-EM structure of pleconaril-resistant rhinovirus-B5 complexed to the antiviral OBR-5-340 reveals unexpected binding site

Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers

Data Resources for the Computer-Guided Discovery of Bioactive Natural Products

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

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

Discovery of Bioactive Natural Products for the Treatment of Acute Respiratory Infections - An Integrated Approach.

Discovery of Novel Natural Neuraminidase Inhibitors (NAI) based on In Silico Screening and Antiviral Investigations

Discovery of nonsteroidal 17beta-hydroxysteroid dehydrogenase 1 inhibitors by pharmacophore-based screening of virtual compound libraries

Discovery of novel CB2 receptor ligands by a pharmacophore-based virtual screening workflow

Discovery of novel PPAR ligands by a virtual screening approach based on pharmacophore modeling, 3D shape, and electrostatic similarity screening

Discovery of novel cathepsin S inhibitors by pharmacophore-based virtual high-throughput screening

Discovery of prenylated flavonoids with dual activity against influenza virus and Streptococcus pneumoniae

Disruption of the viral polymerase complex assembly as a novel approach to attenuate influenza A virus

Dual Acting Neuraminidase Inhibitors Open New Opportunities to Disrupt the Lethal Synergism between Streptococcus pneumoniae and Influenza Virus.

Enhancing drug discovery through in silico screening: strategies to increase true positives retrieval rates.

Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection--what can we learn from earlier mistakes?

FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity

FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes

FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes

Fast and efficient in silico 3D screening: toward maximum computational efficiency of pharmacophore-based and shape-based approaches

From in silico target prediction to multi-target drug design: current databases, methods and applications

GLORY: Generator of the Structures of Likely Cytochrome P450 Metabolites Based on Predicted Sites of Metabolism

GLORYx: Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics

HDAC3i-Finder: A Machine Learning-based Computational Tool to Screen for HDAC3 Inhibitors

High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators

Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters

Hit Dexter: A Machine-learning Model for the Prediction of Frequent Hitters.

How Diverse Are the Protein-Bound Conformations of Small-Molecule Drugs and Cofactors?

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

How do metabolites differ from their parent molecules and how are they excreted?

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

INH14, a Small-Molecule Urea Derivative, Inhibits the IKKα/β-Dependent TLR Inflammatory Response

Identification of HIV-1 Reverse Transcriptase Dual Inhibitors by a Combined Shape-, 2D-Fingerprint- and Pharmacophore-based Virtual Screening Approach

Identification of HIV-1 reverse transcriptase dual inhibitors by a combined shape-, 2D-fingerprint- and pharmacophore-based virtual screening approach

Identification of chemically diverse, novel inhibitors of 17β-hydroxysteroid dehydrogenase type 3 and 5 by pharmacophore-based virtual screening

In Silico Models to Predict the Perturbation of Molecular Initiating Events Related to Thyroid Hormone Homeostasis

Influenza neuraminidase: a druggable target for natural products

Interface dynamics explain assembly dependency of influenza neuraminidase catalytic activity.

Modulators of Protein-Protein Interactions – Novel Approaches in Targeting Protein Kinases and Other Pharmaceutically Relevant Biomolecules ⬇️

Molecular mechanism of a specific capsid binder resistance caused by mutations outside the binding pocket

Morphinans and isoquinolines: acetylcholinesterase inhibition, pharmacophore modeling, and interaction with opioid receptors.

N-thiadiazole-4-hydroxy-2-quinolone-3-carboxamides bearing heteroaromatic rings as novel antibacterial agents: Design, synthesis, biological evaluation and target identification

NERDD: a web portal providing access to in silico tools for drug discovery

NP-Scout: Machine Learning Approach for the Quantification and Visualization of the Natural Product-Likeness of Small Molecules

Natural products against acute respiratory infections: Strategies and lessons learned

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

Novel pharmacological chaperones that correct phenylketonuria in mice.

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

PAIN(S) relievers for medicinal chemists: how computational methods can assist in hit evaluation

Pharmacophore modeling and parallel screening for PPAR ligands