List of works - Matthias Rarey

10th ICCS/GCC Conference: 40 Years of Cheminformatics

scientific article published on 22 June 2015

A Consistent Scheme for Gradient-Based Optimization of Protein<b>-</b>Ligand Poses

scientific article published on 01 December 2020

A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function

scientific article

A fast flexible docking method using an incremental construction algorithm.

scientific article published in August 1996

A flexible-hydrogen interaction model for protein-ligand docking.

scientific article

ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations

scientific article published on 22 June 2015

Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web.

scientific article published on 11 March 2014

Aligning chemical structure diagrams with local search.

scientific article

An integrated approach to knowledge-driven structure-based virtual screening

scientific article

Analyzing the topology of active sites: on the prediction of pockets and subpockets

scientific article published on 14 October 2010

Automated drawing of structural molecular formulas under constraints

scientific article published in May 2004

Benchmark data sets for structure-based computational target prediction

scientific article

Benchmarking Commercial Conformer Ensemble Generators

scientific article

Beyond the virtual screening paradigm: structure-based searching for new lead compounds

scientific article

CASP2 experiences with docking flexible ligands using FlexX.

scientific article published in January 1997

CONFECT: conformations from an expert collection of torsion patterns

scientific article

Chemical pattern visualization in 2D – the SMARTSviewer.

scientific article

Combining global and local measures for structure-based druggability predictions

scientific article published on 5 January 2012

Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis

scientific article published on 24 May 2019

Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms

scientific article published on 23 May 2019

Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation.

scientific article published on 4 October 2017

Computational biotechnology: Prediction of competitive substrate inhibition of enzymes by buffer compounds with protein–ligand docking

Computational methods for biomolecular docking.

scientific article

Conformational sampling for large-scale virtual screening: accuracy versus ensemble size.

scientific article

Conformator: A Novel Method for the Generation of Conformer Ensembles

scientific article published on 12 February 2019

Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration

scientific article published on 25 October 2019

Consistent two-dimensional visualization of protein-ligand complex series

scientific article

De novo design by pharmacophore-based searches in fragment spaces

scientific article published on 16 September 2011

Design of combinatorial libraries for the exploration of virtual hits from fragment space searches with LoFT.

scientific article

Detailed analysis of scoring functions for virtual screening

scientific article

Disconnected Maximum Common Substructures under Constraints

scientific article published on 16 December 2020

Discriminative Chemical Patterns: Automatic and Interactive Design

scientific article published on 13 August 2015

DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment

scientific article published on 23 May 2012

Docking of hydrophobic ligands with interaction-based matching algorithms

scientific article published in March 1999

Drawing the PDB: Protein-Ligand Complexes in Two Dimensions

scientific article published on 31 August 2010

Editorial: Method and Data Sharing and Reproducibility of Scientific Results

scientific article published on 01 December 2020

Elucidating protein-protein interactions using the HYDE scoring function.

scientific article published on 11 March 2014

Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures

scientific article published on 5 October 2017

Evaluation of deoxyhypusine synthase inhibitors targeting BCR-ABL positive leukemias

scientific article

Evidence of water molecules--a statistical evaluation of water molecules based on electron density

scientific article published on 16 March 2015

Exploiting structural information for drug-target assessment

scientific article published on March 2014

Exploration of Ultralarge Compound Collections for Drug Discovery

scientific article published on 14 April 2022

Exploring fragment spaces under multiple physicochemical constraints

scientific article published on 28 June 2007

Exploring structure-activity relationships with three-dimensional matched molecular pairs - A review.

scientific article published on 6 December 2017

FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption

scientific article

Facing the challenges of computational target prediction

scientific article

Facing the challenges of structure-based target prediction by inverse virtual screening

scientific article

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

scientific article (publication date: 12 August 2009)

Fast force field-based optimization of protein-ligand complexes with graphics processor

scientific article published on 22 August 2012

Fast protein binding site comparison via an index-based screening technology

scientific article

Feasibility of Active Machine Learning for Multiclass Compound Classification

scientific article published on 7 January 2016

Feature trees: a new molecular similarity measure based on tree matching

scientific article published in September 1998

Flat and Easy: 2D Depiction of Protein-Ligand Complexes

scientific article published on 21 January 2011

FlexE: efficient molecular docking considering protein structure variations.

scientific article

FlexNovo: structure-based searching in large fragment spaces

scientific article published in August 2006

FlexX-Scan: fast, structure-based virtual screening

scientific article published in November 2004

Flexible docking under pharmacophore type constraints

scientific article published in February 2002

Force-field-based minimizations of protein-ligand complexes in the blink of an eye

scientific article published in March 2013

From Structure Diagrams to Visual Chemical Patterns

article by Karen Schomburg et al published 27 September 2010 in Journal of Chemical Information and Modeling

From activity cliffs to target-specific scoring models and pharmacophore hypotheses

scientific article

From modeling to medicinal chemistry: automatic generation of two-dimensional complex diagrams

scientific article published in June 2007

Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies

scientific article published in March 2006

GeoMine: Interactive Pattern Mining of Protein-Ligand Interfaces in the Protein Data Bank

scientific article published on 31 July 2020

HYDEing the false positives – scoring for lead optimization

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

scientific article published on 16 February 2017

Hydrogen placement in protein-ligand complexes under consideration of tautomerism.

scientific article published on 19 April 2011

Identification of Inhibitors of the Tyrosine Kinase c-Met by Structure-Based Virtual Screening

scientific article published on 17 March 2011

Improving similarity-driven library design: customized matching and regioselective feature trees

scientific article

In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening

article

In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding

scientific article

In silico design, synthesis, and screening of novel deoxyhypusine synthase inhibitors targeting HIV-1 replication

scientific article published on 11 March 2014

Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces

scientific article

Interactive design of generic chemical patterns

scientific article published on 09 February 2013

Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein-Ligand Interfaces

scientific article

Let's talk about rings.

scientific article published on 22 March 2013

Letter from the Editors

Linker-Region Modified Derivatives of the Deoxyhypusine Synthase Inhibitor CNI-1493 Suppress HIV-1 Replication

scientific article published on 3 January 2016

LoFT: similarity-driven multiobjective focused library design

scientific article

MONA - Interactive manipulation of molecule collections

scientific article published on 28 August 2013

MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing

scientific article published on 21 September 2015

Machine Learning in Drug Discovery

scientific article published on 15 August 2018

Machine Learning in Drug Discovery

scientific article published on 01 March 2019

Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces

scientific article published in 2021

Modeling of metal interaction geometries for protein-ligand docking.

scientific article

Molecular complexes at a glance: automated generation of two-dimensional complex diagrams

scientific article published on 21 April 2006

Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention.

scientific article published in July 1997

Multiple-ligand-based virtual screening: methods and applications of the MTree approach

scientific article published in October 2005

NAOMI: on the almost trivial task of reading molecules from different file formats

scientific article published in December 2011

NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures

scientific article published on 11 September 2017

Nearly no Scoring Function Without a Hansch-Analysis

scientific article

Novel technologies for virtual screening

scientific article published on January 2004

On the art of compiling and using 'drug-like' chemical fragment spaces

scientific article published in October 2008

Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples

Placement of medium-sized molecular fragments into active sites of proteins.

scientific article published in February 1996

PoseView -- molecular interaction patterns at a glance.

scientific article published on 4 May 2010

Predicting enzymatic function from global binding site descriptors

scientific article published on 24 December 2012

Prediction of kinase inhibitors cross-reaction on the basis of kinase ATP cavity similarities: a study using PKSIM protein similarity score

scientific article published on 26 March 2008

Prediction of protein mutation effects based on dehydration and hydrogen bonding - A large-scale study

scientific article

Protein pocket and ligand shape comparison and its application in virtual screening.

scientific article published on 27 June 2013

Proteins<i>Plus</i>: a comprehensive collection of web-based molecular modeling tools

scientific article published on 19 April 2022

ProteinsPlus: interactive analysis of protein-ligand binding interfaces

scientific article published on 16 April 2020

Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes

scientific article published on 3 April 2014

Reading PDB: perception of molecules from 3D atomic coordinates

scientific article published on 17 December 2012

Recore: a fast and versatile method for scaffold hopping based on small molecule crystal structure conformations

scientific article published on 17 February 2007

RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases

scientific article

SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles.

scientific article

Scientific competency questions as the basis for semantically enriched open pharmacological space development

scientific article

Searching for recursively defined generic chemical patterns in nonenumerated fragment spaces

scientific article published on 9 July 2013

Searching for substructures in fragment spaces

scientific article published on 12 December 2012

Searching substructures in fragment spaces

Second-generation de novo design: a view from a medicinal chemist perspective

scientific article published on 27 June 2009

Shape-Based Descriptors for Efficient Structure-Based Fragment Growing

scientific article published on 16 November 2020

Similarity searching in large combinatorial chemistry spaces

scientific article published in June 2001

Some thoughts on the “A” in computer-aided molecular design ⬇️

scientific article published on December 13, 2011

Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function

scientific article published on 27 December 2011

SwiFT: an index structure for reduced graph descriptors in virtual screening and clustering

scientific article published on 14 June 2007

Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2

scientific article published on 31 July 2012

Systematic search for pairwise dependencies of torsion angles.

scientific article

TFD: Torsion Fingerprints as a new measure to compare small molecule conformations

scientific article published on 6 June 2012

The Art of Compiling Protein Binding Site Ensembles

scientific article published on 30 May 2016

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.

scientific article published in January 2004

The Internet as Scientific Knowledge Base: Navigating the Chem-Bio Space

scientific article published on 7 August 2012

The particle concept: placing discrete water molecules during protein-ligand docking predictions.

scientific article published in January 1999

The valence state combination model: a generic framework for handling tautomers and protonation states

scientific article published on 3 March 2014

Time-efficient docking of flexible ligands into active sites of proteins.

scientific article published in January 1995

Topological Similarity Search in Large Combinatorial Fragment Spaces

scientific article published on 21 October 2020

Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules.

scientific article published on 17 December 2015

Torsion angle preferences in druglike chemical space: a comprehensive guide

scientific article

TorsionAnalyzer: exploring conformational space

scientific article published in March 2013

Towards an Integrated Description of Hydrogen Bonding and Dehydration: Decreasing False Positives in Virtual Screening with the HYDE Scoring Function

article

TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time

scientific article

Two-stage method for protein-ligand docking

scientific article published in October 1999

UNICON: A Powerful and Easy-to-Use Compound Library Converter

scientific article

Unique ring families: a chemically meaningful description of molecular ring topologies

scientific article published on 8 August 2012

What is the potential of structure-based target prediction methods?

scientific article published in January 2014

Where are the boundaries? Automated pocket detection for druggability studies.

scientific article published on 4 May 2010

mRAISE: an alternative algorithmic approach to ligand-based virtual screening

scientific article

List of works by Matthias Rarey

10th ICCS/GCC Conference: 40 Years of Cheminformatics

A Consistent Scheme for Gradient-Based Optimization of Protein<b>-</b>Ligand Poses

A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function

A fast flexible docking method using an incremental construction algorithm.

A flexible-hydrogen interaction model for protein-ligand docking.

ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations

Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web.

Aligning chemical structure diagrams with local search.

An integrated approach to knowledge-driven structure-based virtual screening

Analyzing the topology of active sites: on the prediction of pockets and subpockets

Automated drawing of structural molecular formulas under constraints

Benchmark data sets for structure-based computational target prediction

Benchmarking Commercial Conformer Ensemble Generators

Beyond the virtual screening paradigm: structure-based searching for new lead compounds

CASP2 experiences with docking flexible ligands using FlexX.

CONFECT: conformations from an expert collection of torsion patterns

Chemical pattern visualization in 2D – the SMARTSviewer.

Combining global and local measures for structure-based druggability predictions

Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis

Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms

Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation.

Computational biotechnology: Prediction of competitive substrate inhibition of enzymes by buffer compounds with protein–ligand docking

Computational methods for biomolecular docking.

Conformational sampling for large-scale virtual screening: accuracy versus ensemble size.

Conformator: A Novel Method for the Generation of Conformer Ensembles

Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration

Consistent two-dimensional visualization of protein-ligand complex series

De novo design by pharmacophore-based searches in fragment spaces

Design of combinatorial libraries for the exploration of virtual hits from fragment space searches with LoFT.

Detailed analysis of scoring functions for virtual screening

Disconnected Maximum Common Substructures under Constraints

Discriminative Chemical Patterns: Automatic and Interactive Design

DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment

Docking of hydrophobic ligands with interaction-based matching algorithms

Drawing the PDB: Protein-Ligand Complexes in Two Dimensions

Editorial: Method and Data Sharing and Reproducibility of Scientific Results

Elucidating protein-protein interactions using the HYDE scoring function.

Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures

Evaluation of deoxyhypusine synthase inhibitors targeting BCR-ABL positive leukemias

Evidence of water molecules--a statistical evaluation of water molecules based on electron density

Exploiting structural information for drug-target assessment

Exploration of Ultralarge Compound Collections for Drug Discovery

Exploring fragment spaces under multiple physicochemical constraints

Exploring structure-activity relationships with three-dimensional matched molecular pairs - A review.

FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption

Facing the challenges of computational target prediction

Facing the challenges of structure-based target prediction by inverse virtual screening

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

Fast force field-based optimization of protein-ligand complexes with graphics processor

Fast protein binding site comparison via an index-based screening technology

Feasibility of Active Machine Learning for Multiclass Compound Classification

Feature trees: a new molecular similarity measure based on tree matching

Flat and Easy: 2D Depiction of Protein-Ligand Complexes

FlexE: efficient molecular docking considering protein structure variations.

FlexNovo: structure-based searching in large fragment spaces

FlexX-Scan: fast, structure-based virtual screening

Flexible docking under pharmacophore type constraints

Force-field-based minimizations of protein-ligand complexes in the blink of an eye

From Structure Diagrams to Visual Chemical Patterns

From activity cliffs to target-specific scoring models and pharmacophore hypotheses

From modeling to medicinal chemistry: automatic generation of two-dimensional complex diagrams

Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies

GeoMine: Interactive Pattern Mining of Protein-Ligand Interfaces in the Protein Data Bank

HYDEing the false positives – scoring for lead optimization

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

Hydrogen placement in protein-ligand complexes under consideration of tautomerism.

Identification of Inhibitors of the Tyrosine Kinase c-Met by Structure-Based Virtual Screening

Improving similarity-driven library design: customized matching and regioselective feature trees

In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening

In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding

In silico design, synthesis, and screening of novel deoxyhypusine synthase inhibitors targeting HIV-1 replication

Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces

Interactive design of generic chemical patterns

Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein-Ligand Interfaces

Let's talk about rings.

Letter from the Editors

Linker-Region Modified Derivatives of the Deoxyhypusine Synthase Inhibitor CNI-1493 Suppress HIV-1 Replication

LoFT: similarity-driven multiobjective focused library design

MONA - Interactive manipulation of molecule collections