Matthias Rarey

J. Chem. Inf. Model., 2024

Database-Driven Identification of Structurally Similar Protein-Protein Interfaces.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2024

2023

School of cheminformatics in Latin America.

[BibT_eX]

[DOI]

Karla Gonzalez-Ponce

Carolina Horta Andrade

Fiona M. I. Hunter

Johannes Kirchmair

Karina Martínez-Mayorga

José L. Medina-Franco

J. Cheminformatics, December, 2023

Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead Structures.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., November, 2023

PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., October, 2023

Searching similar local 3D micro-environments in protein structure databases with MicroMiner.

[BibT_eX]

[DOI]

Jochen Sieg

Briefings Bioinform., September, 2023

Single mutation protein structure pairs extracted from the PDB with MicroMiner.

[BibT_eX]

[DOI]

Jochen Sieg

Dataset, September, 2023

Optimization and Evaluation Datasets for PiMine.

[BibT_eX]

[DOI]

Dataset, September, 2023

Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3.

[BibT_eX]

[DOI]

Joel Graef

Christiane Ehrt

J. Chem. Inf. Model., May, 2023

Modeling with Alternate Locations in X-ray Protein Structures.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., April, 2023

Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., January, 2023

Database and Workflow Optimizations for Spatial-Geometric Queries in GeoMine.

[BibT_eX]

[DOI]

Proceedings of the Lernen, 2023

2022

ProteinsPlus: a comprehensive collection of web-based molecular modeling tools.

[BibT_eX]

[DOI]

Katrin Schöning-Stierand

Nucleic Acids Res., 2022

Exploration of Ultralarge Compound Collections for Drug Discovery.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2022

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

[BibT_eX]

[DOI]

Robert Schmidt

Raphael Klein

J. Chem. Inf. Model., 2022

Special Issue on Reaction Informatics and Chemical Space.

[BibT_eX]

[DOI]

Marc C. Nicklaus

Wendy A. Warr

J. Chem. Inf. Model., 2022

The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2022

Interpretation of Structure-Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2022

Visualizing Generic Reaction Patterns.

[BibT_eX]

[DOI]

Uschi Dolfus

Hans Briem

J. Chem. Inf. Model., 2022

Synthesis-Aware Generation of Structural Analogues.

[BibT_eX]

[DOI]

Uschi Dolfus

Hans Briem

J. Chem. Inf. Model., 2022

Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2022

Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces.

[BibT_eX]

[DOI]

Louis Bellmann

Raphael Klein

J. Chem. Inf. Model., 2022

FastGrow: on-the-fly growing and its application to DYRK1A.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2022

2021

Disconnected Maximum Common Substructures under Constraints.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2021

Call for Papers for the Special Issue: From Reaction Informatics to Chemical Space.

[BibT_eX]

[DOI]

Marc C. Nicklaus

Wendy A. Warr

J. Chem. Inf. Model., 2021

Topological Similarity Search in Large Combinatorial Fragment Spaces.

[BibT_eX]

[DOI]

Louis Bellmann

Patrick Penner

J. Chem. Inf. Model., 2021

LSLOpt: An open-source implementation of the step-length controlled LSL-BFGS algorithm.

[BibT_eX]

[DOI]

Florian Flachsenberg

J. Comput. Chem., 2021

GeoMine: interactive pattern mining of protein-ligand interfaces in the Protein Data Bank.

[BibT_eX]

[DOI]

Konrad Diedrich

Joel Graef

Katrin Schöning-Stierand

Bioinform., 2021

2020

ProteinsPlus: interactive analysis of protein-ligand binding interfaces.

[BibT_eX]

[DOI]

Katrin Schöning-Stierand

Nucleic Acids Res., 2020

Shape-Based Descriptors for Efficient Structure-Based Fragment Growing.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2020

Editorial: Method and Data Sharing and Reproducibility of Scientific Results.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2020

A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2020

2019

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

[BibT_eX]

[DOI]

Jochen Sieg

Florian Flachsenberg

J. Chem. Inf. Model., 2019

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

[BibT_eX]

[DOI]

Robert Schmidt

Emanuel S. R. Ehmki

Farina Ohm

Andriy Mashychev

J. Chem. Inf. Model., 2019

Conformator: A Novel Method for the Generation of Conformer Ensembles.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2019

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

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2019

Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration.

[BibT_eX]

[DOI]

Louis Bellmann

Patrick Penner

J. Chem. Inf. Model., 2019

StructureProfiler: an all-in-one tool for 3D protein structure profiling.

[BibT_eX]

[DOI]

Bioinform., 2019

2018

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

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2018

Machine Learning in Drug Discovery.

[BibT_eX]

[DOI]

Sepp Hochreiter

Günter Klambauer

J. Chem. Inf. Model., 2018

2017

Benchmarking Commercial Conformer Ensemble Generators.

[BibT_eX]

[DOI]

Nils-Ole Friedrich

Christina de Bruyn Kops

J. Chem. Inf. Model., November, 2017

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

[BibT_eX]

[DOI]

J. Chem. Inf. Model., October, 2017

NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., September, 2017

ProteinsPlus: a web portal for structure analysis of macromolecules.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2017

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

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2017

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

[BibT_eX]

[DOI]

Nils-Ole Friedrich

Agnes Meyder

Christina de Bruyn Kops

J. Chem. Inf. Model., 2017

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

[BibT_eX]

[DOI]

Florian Flachsenberg

Niek Andresen

J. Chem. Inf. Model., 2017

Ligand-based virtual screening under partial shape constraints.

[BibT_eX]

[DOI]

Mathias M. von Behren

J. Comput. Aided Mol. Des., 2017

2016

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

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2016

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

[BibT_eX]

[DOI]

Florian Lauck

J. Chem. Inf. Model., 2016

Feasibility of Active Machine Learning for Multiclass Compound Classification.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2016

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

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2016

SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2016

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

[BibT_eX]

[DOI]

Mathias M. von Behren

Eva Nittinger

J. Comput. Aided Mol. Des., 2016

2015

10th ICCS/GCC Conference: 40 Years of Cheminformatics.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2015

Evidence of Water Molecules - A Statistical Evaluation of Water Molecules Based on Electron Density.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2015

Letter from the Editors.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2015

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

[BibT_eX]

[DOI]

Matthias Hilbig

J. Chem. Inf. Model., 2015

Discriminative Chemical Patterns: Automatic and Interactive Design.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2015

ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2015

2014

The Valence State Combination Model: A Generic Framework for Handling Tautomers and Protonation States.

[BibT_eX]

[DOI]

Adrian Kolodzik

J. Chem. Inf. Model., 2014

Benchmark Data Sets for Structure-Based Computational Target Prediction.

[BibT_eX]

[DOI]

Karen Schomburg

J. Chem. Inf. Model., 2014

Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2014

Elucidating protein-protein interactions using the HYDE scoring function.

[BibT_eX]

[DOI]

J. Cheminformatics, 2014

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

[BibT_eX]

[DOI]

J. Cheminformatics, 2014

Facing the challenges of computational target prediction.

[BibT_eX]

[DOI]

Karen T. Schomburg

J. Cheminformatics, 2014

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

[BibT_eX]

[DOI]

J. Cheminformatics, 2014

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

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2014

2013

Reading PDB: Perception of Molecules from 3D Atomic Coordinates.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2013

Searching for Recursively Defined Generic Chemical Patterns in Nonenumerated Fragment Spaces.

[BibT_eX]

[DOI]

Angela M. Henzler

J. Chem. Inf. Model., 2013

Fast Protein Binding Site Comparison via an Index-Based Screening Technology.

[BibT_eX]

[DOI]

Mathias M. von Behren

J. Chem. Inf. Model., 2013

TorsionAnalyzer: exploring conformational space.

[BibT_eX]

[DOI]

Christin Schärfer

Tanja Schulz-Gasch

J. Cheminformatics, 2013

Let's talk about rings.

[BibT_eX]

[DOI]

Adrian Kolodzik

J. Cheminformatics, 2013

MONA - Interactive manipulation of molecule collections.

[BibT_eX]

[DOI]

J. Cheminformatics, 2013

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

[BibT_eX]

[DOI]

Lennart Heinzerling

J. Cheminformatics, 2013

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

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2013

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

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2013

2012

Combining Global and Local Measures for Structure-Based Druggability Predictions.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2012

TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2012

Design of Combinatorial Libraries for the Exploration of Virtual Hits from Fragment Space Searches with LoFT.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2012

Unique Ring Families: A Chemically Meaningful Description of Molecular Ring Topologies.

[BibT_eX]

[DOI]

Adrian Kolodzik

J. Chem. Inf. Model., 2012

Searching for Substructures in Fragment Spaces.

[BibT_eX]

[DOI]

Andrea Volkamer

J. Chem. Inf. Model., 2012

Systematic search for pairwise dependencies of torsion angles.

[BibT_eX]

[DOI]

Christin Schärfer

Tanja Schulz-Gasch

J. Cheminformatics, 2012

Aligning chemical structure diagrams with local search.

[BibT_eX]

[DOI]

Matthias Hilbig

J. Cheminformatics, 2012

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

[BibT_eX]

[DOI]

J. Cheminformatics, 2012

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

[BibT_eX]

[DOI]

J. Cheminformatics, 2012

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

[BibT_eX]

[DOI]

Lennart Heinzerling

Robert Klein

J. Comput. Chem., 2012

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

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2012

Some thoughts on the "A" in computer-aided molecular design.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2012

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

[BibT_eX]

[DOI]

Bioinform., 2012

2011

NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2011

Improving Similarity-Driven Library Design: Customized Matching and Regioselective Feature Trees.

[BibT_eX]

[DOI]

J. Robert Fischer

Uta F. Lessel

J. Chem. Inf. Model., 2011

Consistent two-dimensional visualization of protein-ligand complex series.

[BibT_eX]

[DOI]

J. Cheminformatics, 2011

Chemical pattern visualization in 2D - the SMARTSviewer.

[BibT_eX]

[DOI]

Karen Schomburg

J. Cheminformatics, 2011

HYDEing the false positives - scoring for lead optimization.

[BibT_eX]

[DOI]

J. Cheminformatics, 2011

Searching substructures in fragment spaces.

[BibT_eX]

[DOI]

J. Cheminformatics, 2011

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

[BibT_eX]

[DOI]

J. Cheminformatics, 2011

De novo design by pharmacophore-based searches in fragment spaces.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2011

2010

Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2010

From Structure Diagrams to Visual Chemical Patterns.

[BibT_eX]

[DOI]

Karen Schomburg

J. Chem. Inf. Model., 2010

LoFT: Similarity-Driven Multiobjective Focused Library Design.

[BibT_eX]

[DOI]

J. Robert Fischer

Uta F. Lessel

J. Chem. Inf. Model., 2010

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

[BibT_eX]

[DOI]

Andrea Volkamer

Thomas Grombacher

J. Cheminformatics, 2010

PoseView - molecular interaction patterns at a glance.

[BibT_eX]

[DOI]

J. Cheminformatics, 2010

2009

Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds.

[BibT_eX]

[DOI]

Jochen Schlosser

J. Chem. Inf. Model., 2009

Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2009

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

[BibT_eX]

[DOI]

Tobias Lippert

J. Cheminformatics, 2009

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

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2009

2007

Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2007

SwiFT: An Index Structure for Reduced Graph Descriptors in Virtual Screening and Clustering.

[BibT_eX]

[DOI]

J. Robert Fischer

J. Chem. Inf. Model., 2007

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

[BibT_eX]

[DOI]

Ingo Schellhammer

J. Comput. Aided Mol. Des., 2007

Exploring fragment spaces under multiple physicochemical constraints.

[BibT_eX]

[DOI]

Juri Pärn

Jörg Degen

J. Comput. Aided Mol. Des., 2007

2006

Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2006

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

[BibT_eX]

[DOI]

Patrick C. Maaß

Bioinform., 2006

2005

From greedy to branch & bound and back: Assessing optimization strategies for incremental construction molecular docking tools.

[BibT_eX]

[DOI]

Axel Griewel

Proceedings of the German Conference on Bioinformatics (GCB 2005), Hamburg, 2005

2004

Automated Drawing of Structural Molecular Formulas under Constraints.

[BibT_eX]

[DOI]

Patrick C. Fricker

Marcus Gastreich

J. Chem. Inf. Model., 2004

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

[BibT_eX]

[DOI]

Bioinform., 2004

2002

Flexible docking under pharmacophore type constraints.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2002

Geometric Problems and Algorithms in Computer-Aided Molecular Design.

[BibT_eX]

[DOI]

Proceedings of the 32. Jahrestagung der Gesellschaft für Informatik, Informatik bewegt, INFORMATIK 2002, Dortmund, Germany, September 30, 2002

2001

Similarity searching in large combinatorial chemistry spaces.

[BibT_eX]

[DOI]

Martin Stahl

J. Comput. Aided Mol. Des., 2001

Algorithmen für den computergestützten Wirkstoffentwurf.

[BibT_eX]

GMD research series 22, GMD, ISBN: 978-3-88457-405-8, 2001

1999

Docking of hydrophobic ligands with interaction-based matching algorithms.

[BibT_eX]

[DOI]

Bernd Kramer

Bioinform., 1999

1998

Feature trees: A new molecular similarity measure based on tree matching.

[BibT_eX]

[DOI]

J. Scott Dixon

J. Comput. Aided Mol. Des., 1998

1997

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

[BibT_eX]

[DOI]

Bernd Kramer

J. Comput. Aided Mol. Des., 1997

1996

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

[BibT_eX]

[DOI]

Stephan Wefing

J. Comput. Aided Mol. Des., 1996

Rechnergestützte Vorhersage von Rezeptor-Ligand-Wechselwirkungen.

[BibT_eX]

GMD-Bericht 268, Oldenbourg, ISBN: 978-3-486-24010-8, 1996

1995

Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins.

[BibT_eX]

[DOI]

Bernd Kramer