Prediction of the three-dimensional structure of the human Fas receptor by comparative molecular modeling. - Jürgen Bajorath; Alejandro Aruffo (J. Comput. Aided Mol. Des., 1997)

Computer-Aided Drug Design - Session Introduction. - Jürgen Bajorath; Teri E. Klein; Terry P. Lybrand; Jiri Novotny (Pacific Symposium on Biocomputing, 1999)

Analysis of Fas-ligand interactions using a molecular model of the receptor-ligand interface. - Jürgen Bajorath (J. Comput. Aided Mol. Des., 1999)

Statistical analysis of computational docking of large compound data bases to distinct protein binding sites. - Jeffrey W. Godden; Florence L. Stahura; Jürgen Bajorath (J. Comput. Chem., 1999)

Binary Quantitative Structure-Activity Relationship (QSAR) Analysis of Estrogen Receptor Ligands. - Hua Gao; Christopher I. Williams; Paul Labute; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 1999)

Database Searching for Compounds with Similar Biological Activity Using Short Binary Bit String Representations of Molecules. - Ling Xue; Jeffrey W. Godden; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 1999)

Identification of a Preferred Set of Molecular Descriptors for Compound Classification Based on Principal Component Analysis. - Ling Xue; Jeffrey W. Godden; Hua Gao; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 1999)

Molecular Descriptors for Effective Classification of Biologically Active Compounds Based on Principal Component Analysis Identified by a Genetic Algorithm. - Ling Xue; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2000)

Variability of Molecular Descriptors in Compound Databases Revealed by Shannon Entropy Calculations. - Jeffrey W. Godden; Florence L. Stahura; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2000)

Combinatorial Preferences Affect Molecular Similarity/Diversity Calculations Using Binary Fingerprints and Tanimoto Coefficients. - Jeffrey W. Godden; Ling Xue; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2000)

Distinguishing between Natural Products and Synthetic Molecules by Descriptor Shannon Entropy Analysis and Binary QSAR Calculations. - Florence L. Stahura; Jeffrey W. Godden; Ling Xue; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2000)

Evaluation of Descriptors and Mini-Fingerprints for the Identification of Molecules with Similar Activity. - Ling Xue; Jeffrey W. Godden; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2000)

Selected Concepts and Investigations in Compound Classification, Molecular Descriptor Analysis, and Virtual Screening. - Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2001)

Differential Shannon Entropy as a Sensitive Measure of Differences in Database Variability of Molecular Descriptors. - Jeffrey W. Godden; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2001)

Mini-fingerprints Detect Similar Activity of Receptor Ligands Previously Recognized Only by Three-Dimensional Pharmacophore-Based Methods. - Ling Xue; Florence L. Stahura; Jeffrey W. Godden; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2001)

Fingerprint Scaling Increases the Probability of Identifying Molecules with Similar Activity in Virtual Screening Calculations. - Ling Xue; Florence L. Stahura; Jeffrey W. Godden; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2001)

Chemoinformatics methods for systematic comparison of molecules from natural and synthetic sources and design of hybrid libraries. - Jürgen Bajorath (J. Comput. Aided Mol. Des., 2002)

Chemical Descriptors with Distinct Levels of Information Content and Varying Sensitivity to Differences between Selected Compound Databases Identified by SE-DSE Analysis. - Jeffrey W. Godden; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2002)

Classification of Biologically Active Compounds by Median Partitioning. - Jeffrey W. Godden; Ling Xue; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2002)

Median Partitioning: A Novel Method for the Selection of Representative Subsets from Large Compound Pools. - Jeffrey W. Godden; Ling Xue; Douglas B. Kitchen; Florence L. Stahura; E. James Schermerhorn; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2002)

Differential Shannon Entropy Analysis Identifies Molecular Property Descriptors that Predict Aqueous Solubility of Synthetic Compounds with High Accuracy in Binary QSAR Calculations. - Florence L. Stahura; Jeffrey W. Godden; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2002)

Accurate Partitioning of Compounds Belonging to Diverse Activity Classes. - Ling Xue; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2002)

Recursive Median Partitioning for Virtual Screening of Large Databases. - Jeffrey W. Godden; John R. Furr; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2003)

Design and Evaluation of a Molecular Fingerprint Involving the Transformation of Property Descriptor Values into a Binary Classification Scheme. - Ling Xue; Jeffrey W. Godden; Florence L. Stahura; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2003)

Profile Scaling Increases the Similarity Search Performance of Molecular Fingerprints Containing Numerical Descriptors and Structural Keys. - Ling Xue; Jeffrey W. Godden; Florence L. Stahura; Jürgen Bajorath (J. Chem. Inf. Comput. Sci., 2003)

Molecular Similarity Analysis and Virtual Screening by Mapping of Consensus Positions in Binary-Transformed Chemical Descriptor Spaces with Variable Dimensionality. - Jeffrey W. Godden; John R. Furr; Ling Xue; Florence L. Stahura; Jürgen Bajorath (J. Chem. Inf. Model., 2004)

Similarity Search Profiles as a Diagnostic Tool for the Analysis of Virtual Screening Calculations. - Ling Xue; Jeffrey W. Godden; Florence L. Stahura; Jürgen Bajorath (J. Chem. Inf. Model., 2004)

Similarity Search Profiling Reveals Effects of Fingerprint Scaling in Virtual Screening. - Ling Xue; Florence L. Stahura; Jürgen Bajorath (J. Chem. Inf. Model., 2004)

Anatomy of Fingerprint Search Calculations on Structurally Diverse Sets of Active Compounds. - Jeffrey W. Godden; Florence L. Stahura; Jürgen Bajorath (J. Chem. Inf. Model., 2005)

Emerging Chemical Patterns: A New Methodology for Molecular Classification and Compound Selection. - Jens Auer; Jürgen Bajorath (J. Chem. Inf. Model., 2006)

Assessment of Molecular Similarity from the Analysis of Randomly Generated Structural Fragment Populations. - José Batista; Jeffrey W. Godden; Jürgen Bajorath (J. Chem. Inf. Model., 2006)

Design and Evaluation of a Novel Class-Directed 2D Fingerprint to Search for Structurally Diverse Active Compounds. - Hanna Eckert; Jürgen Bajorath (J. Chem. Inf. Model., 2006)

Mapping Algorithms for Molecular Similarity Analysis and Ligand-Based Virtual Screening: Design of DynaMAD and Comparison with MAD and DMC. - Hanna Eckert; Ingo Vogt; Jürgen Bajorath (J. Chem. Inf. Model., 2006)

A Distance Function for Retrieval of Active Molecules from Complex Chemical Space Representations. - Jeffrey W. Godden; Jürgen Bajorath (J. Chem. Inf. Model., 2006)

Chemical Database Mining through Entropy-Based Molecular Similarity Assessment of Randomly Generated Structural Fragment Populations. - José Batista; Jürgen Bajorath (J. Chem. Inf. Model., 2007)

Mining of Randomly Generated Molecular Fragment Populations Uncovers Activity-Specific Fragment Hierarchies. - José Batista; Jürgen Bajorath (J. Chem. Inf. Model., 2007)

Exploring Peptide-likeness of Active Molecules Using 2D Fingerprint Methods. - Hanna Eckert; Jürgen Bajorath (J. Chem. Inf. Model., 2007)

Mapping of Activity-Specific Fragment Pathways Isolated from Random Fragment Populations Reveals the Formation of Coherent Molecular Cores. - Eugen Lounkine; José Batista; Jürgen Bajorath (J. Chem. Inf. Model., 2007)

Introduction of an Information-Theoretic Method to Predict Recovery Rates of Active Compounds for Bayesian in Silico Screening: Theory and Screening Trials. - Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2007)

Analysis of a High-Throughput Screening Data Set Using Potency-Scaled Molecular Similarity Algorithms. - Ingo Vogt; Jürgen Bajorath (J. Chem. Inf. Model., 2007)

Bayesian Interpretation of a Distance Function for Navigating High-Dimensional Descriptor Spaces. - Martin Vogt 001; Jeffrey W. Godden; Jürgen Bajorath (J. Chem. Inf. Model., 2007)

Distinguishing between Bioactive and Modeled Compound Conformations through Mining of Emerging Chemical Patterns. - Jens Auer; Jürgen Bajorath (J. Chem. Inf. Model., 2008)

Ligand-Target Interaction-Based Weighting of Substructures for Virtual Screening. - Thomas J. Crisman; Mihiret Tekeste Sisay; Jürgen Bajorath (J. Chem. Inf. Model., 2008)

Support-Vector-Machine-Based Ranking Significantly Improves the Effectiveness of Similarity Searching Using 2D Fingerprints and Multiple Reference Compounds. - Hanna Geppert; Tamás Horváth 001; Thomas Gärtner 001; Stefan Wrobel; Jürgen Bajorath (J. Chem. Inf. Model., 2008)

Core Trees and Consensus Fragment Sequences for Molecular Representation and Similarity Analysis. - Eugen Lounkine; Jürgen Bajorath (J. Chem. Inf. Model., 2008)

Similarity Searching Using Fingerprints of Molecular Fragments Involved in Protein-Ligand Interactions. - Lu Tan; Eugen Lounkine; Jürgen Bajorath (J. Chem. Inf. Model., 2008)

Bayesian Similarity Searching in High-Dimensional Descriptor Spaces Combined with Kullback-Leibler Descriptor Divergence Analysis. - Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2008)

Design and Exploration of Target-Selective Chemical Space Representations. - Ingo Vogt; Jürgen Bajorath (J. Chem. Inf. Model., 2008)

Balancing the Influence of Molecular Complexity on Fingerprint Similarity Searching. - Yuan Wang; Jürgen Bajorath (J. Chem. Inf. Model., 2008)

Bit Silencing in Fingerprints Enables the Derivation of Compound Class-Directed Similarity Metrics. - Yuan Wang; Jürgen Bajorath (J. Chem. Inf. Model., 2008)

Ligand Prediction from Protein Sequence and Small Molecule Information Using Support Vector Machines and Fingerprint Descriptors. - Hanna Geppert; Jens Humrich; Dagmar Stumpfe; Thomas Gärtner 001; Jürgen Bajorath (J. Chem. Inf. Model., 2009)

Topological Fragment Index for the Analysis of Molecular Substructures and Their Topological Environment in Active Compounds. - Eugen Lounkine; Jürgen Bajorath (J. Chem. Inf. Model., 2009)

Relevance of Feature Combinations for Similarity Searching Using General or Activity Class-Directed Molecular Fingerprints. - Eugen Lounkine; Ye Hu; José Batista; Jürgen Bajorath (J. Chem. Inf. Model., 2009)

Molecular Formal Concept Analysis for Compound Selectivity Profiling in Biologically Annotated Databases. - Eugen Lounkine; Dagmar Stumpfe; Jürgen Bajorath (J. Chem. Inf. Model., 2009)

Development of a Fingerprint Reduction Approach for Bayesian Similarity Searching Based on Kullback-Leibler Divergence Analysis. - Britta Nisius; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2009)

Structural Interpretation of Activity Cliffs Revealed by Systematic Analysis of Structure-Activity Relationships in Analog Series. - Mihiret Tekeste Sisay; Lisa Peltason; Jürgen Bajorath (J. Chem. Inf. Model., 2009)

Development of a Compound Class-Directed Similarity Coefficient That Accounts for Molecular Complexity Effects in Fingerprint Searching. - Yuan Wang; Jürgen Bajorath (J. Chem. Inf. Model., 2009)

Shannon Entropy-Based Fingerprint Similarity Search Strategy. - Yuan Wang; Hanna Geppert; Jürgen Bajorath (J. Chem. Inf. Model., 2009)

Searching for Target-Selective Compounds Using Different Combinations of Multiclass Support Vector Machine Ranking Methods, Kernel Functions, and Fingerprint Descriptors. - Anne Mai Wassermann; Hanna Geppert; Jürgen Bajorath (J. Chem. Inf. Model., 2009)

Ligand Prediction for Orphan Targets Using Support Vector Machines and Various Target-Ligand Kernels Is Dominated by Nearest Neighbor Effects. - Anne Mai Wassermann; Hanna Geppert; Jürgen Bajorath (J. Chem. Inf. Model., 2009)

Predicting the similarity search performance of fingerprints and their combination with molecular property descriptors using probabilistic and information theoretic modeling. - Martin Vogt 001; Britta Nisius; Jürgen Bajorath (Stat. Anal. Data Min., 2009)

Application of Information - Theoretic Concepts in Chemoinformatics. - Martin Vogt 001; Anne Mai Wassermann; Jürgen Bajorath (Inf., 2010)

Adaptation of formal concept analysis for the systematic exploration of structure-activity and structure-selectivity relationships. - Eugen Lounkine; Jürgen Bajorath (J. Cheminformatics, 2010)

Systematic extraction of structure-activity relationship information from biological screening data. - Mathias Wawer; Lisa Peltason; Jürgen Bajorath (J. Cheminformatics, 2010)

Design and Evaluation of Bonded Atom Pair Descriptors. - Hany E. A. Ahmed; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2010)

Atom-Centered Interacting Fragments and Similarity Search Applications. - José Batista; Lu Tan; Jürgen Bajorath (J. Chem. Inf. Model., 2010)

Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation. - Hanna Geppert; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2010)

Molecular Scaffolds with High Propensity to Form Multi-Target Activity Cliffs. - Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2010)

Polypharmacology Directed Compound Data Mining: Identification of Promiscuous Chemotypes with Different Activity Profiles and Comparison to Approved Drugs. - Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2010)

SARANEA: A Freely Available Program To Mine Structure-Activity and Structure-Selectivity Relationship Information in Compound Data Sets. - Eugen Lounkine; Mathias Wawer; Anne Mai Wassermann; Jürgen Bajorath (J. Chem. Inf. Model., 2010)

Rationalizing Three-Dimensional Activity Landscapes and the Influence of Molecular Representations on Landscape Topology and the Formation of Activity Cliffs. - Lisa Peltason; Preeti Iyer; Jürgen Bajorath (J. Chem. Inf. Model., 2010)

Rationalization of the Performance and Target Dependence of Similarity Searching Incorporating Protein-Ligand Interaction Information. - Lu Tan; José Batista; Jürgen Bajorath (J. Chem. Inf. Model., 2010)

Chemical Substitutions That Introduce Activity Cliffs Across Different Compound Classes and Biological Targets. - Anne Mai Wassermann; Jürgen Bajorath (J. Chem. Inf. Model., 2010)

Identification of Descriptors Capturing Compound Class-Specific Features by Mutual Information Analysis. - Anne Mai Wassermann; Britta Nisius; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2010)

Similarity-Potency Trees: A Method to Search for SAR Information in Compound Data Sets and Derive SAR Rules. - Mathias Wawer; Jürgen Bajorath (J. Chem. Inf. Model., 2010)

Design of Multitarget Activity Landscapes That Capture Hierarchical Activity Cliff Distributions. - Dilyana Dimova; Mathias Wawer; Anne Mai Wassermann; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Large-Scale Similarity Search Profiling of ChEMBL Compound Data Sets. - Kathrin Heikamp; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

How Do 2D Fingerprints Detect Structurally Diverse Active Compounds? Revealing Compound Subset-Specific Fingerprint Features through Systematic Selection. - Kathrin Heikamp; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Combining Horizontal and Vertical Substructure Relationships in Scaffold Hierarchies for Activity Prediction. - Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Target Family-Directed Exploration of Scaffolds with Different SAR Profiles. - Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Lessons Learned from Molecular Scaffold Analysis. - Ye Hu; Dagmar Stumpfe; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

SAR Monitoring of Evolving Compound Data Sets Using Activity Landscapes. - Preeti Iyer; Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Molecular Mechanism-Based Network-like Similarity Graphs Reveal Relationships between Different Types of Receptor Ligands and Structural Changes that Determine Agonistic, Inverse-Agonistic, and Antagonistic Effects. - Preeti Iyer; Dagmar Stumpfe; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Development of a Method To Consistently Quantify the Structural Distance between Scaffolds and To Assess Scaffold Hopping Potential. - Ruifang Li; Dagmar Stumpfe; Martin Vogt 001; Hanna Geppert; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Extraction of Discontinuous Structure-Activity Relationships from Compound Data Sets through Particle Swarm Optimization. - Vigneshwaran Namasivayam; Preeti Iyer; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Rationalizing the Role of SAR Tolerance for Ligand-Based Virtual Screening. - Peter Ripphausen; Britta Nisius; Mathias Wawer; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

REPROVIS-DB: A Benchmark System for Ligand-Based Virtual Screening Derived from Reproducible Prospective Applications. - Peter Ripphausen; Anne Mai Wassermann; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Assessing the Confidence Level of Public Domain Compound Activity Data and the Impact of Alternative Potency Measurements on SAR Analysis. - Dagmar Stumpfe; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Introduction of the Conditional Correlated Bernoulli Model of Similarity Value Distributions and its Application to the Prospective Prediction of Fingerprint Search Performance. - Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

From Activity Cliffs to Activity Ridges: Informative Data Structures for SAR Analysis. - Martin Vogt 001; Yun Huang; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

A Data Mining Method To Facilitate SAR Transfer. - Anne Mai Wassermann; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Correction to Identification of Descriptors Capturing Compound Class-Specific Features by Mutual Information Analysis. - Anne Mai Wassermann; Britta Nisius; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2011)

Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications. - Ye Hu; Jürgen Bajorath (F1000Research, 2012)

Computational chemistry in pharmaceutical research: at the crossroads. - Jürgen Bajorath (J. Comput. Aided Mol. Des., 2012)

Systematic assessment of scaffold distances in ChEMBL: prioritization of compound data sets for scaffold hopping analysis in virtual screening. - Ruifang Li; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2012)

Design of multi-target activity landscapes that capture hierarchical activity cliff distributions. - Dilyana Dimova; Jürgen Bajorath (J. Cheminformatics, 2012)

Potency-directed similarity searching using support vector machines. - Kathrin Heikamp; Anne Mai Wassermann; Jürgen Bajorath (J. Cheminformatics, 2012)

A computational method to facilitate structure-activity relationship transfer. - Anne Mai Wassermann; Jürgen Bajorath (J. Cheminformatics, 2012)

Identification of Multitarget Activity Ridges in High-Dimensional Bioactivity Spaces. - Disha Gupta-Ostermann; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Graph Mining for SAR Transfer Series. - Disha Gupta-Ostermann; Mathias Wawer; Anne Mai Wassermann; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Prediction of Activity Cliffs Using Support Vector Machines. - Kathrin Heikamp; Xiaoying Hu; Aixia Yan; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Exploration of 3D Activity Cliffs on the Basis of Compound Binding Modes and Comparison of 2D and 3D Cliffs. - Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Extending the Activity Cliff Concept: Structural Categorization of Activity Cliffs and Systematic Identification of Different Types of Cliffs in the ChEMBL Database. - Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Growth of Ligand-Target Interaction Data in ChEMBL Is Associated with Increasing and Activity Measurement-Dependent Compound Promiscuity. - Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Systematic Identification and Classification of Three-Dimensional Activity Cliffs. - Ye Hu; Norbert Furtmann; Michael Gütschow; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

MMP-Cliffs: Systematic Identification of Activity Cliffs on the Basis of Matched Molecular Pairs. - Xiaoying Hu; Ye Hu; Martin Vogt 001; Dagmar Stumpfe; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Navigating High-Dimensional Activity Landscapes: Design and Application of the Ligand-Target Differentiation Map. - Preeti Iyer; Dilyana Dimova; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Design of a Three-Dimensional Multitarget Activity Landscape. - Antonio de la Vega de León; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Searching for Coordinated Activity Cliffs Using Particle Swarm Optimization. - Vigneshwaran Namasivayam; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Multiobjective Particle Swarm Optimization: Automated Identification of Structure-Activity Relationship-Informative Compounds with Favorable Physicochemical Property Distributions. - Vigneshwaran Namasivayam; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Frequency of Occurrence and Potency Range Distribution of Activity Cliffs in Bioactive Compounds. - Dagmar Stumpfe; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

SAR Matrices: Automated Extraction of Information-Rich SAR Tables from Large Compound Data Sets. - Anne Mai Wassermann; Peter Haebel; Nils Weskamp; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Systematic Assessment of Compound Series with SAR Transfer Potential. - Bijun Zhang; Anne Mai Wassermann; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2012)

Emerging Chemical Patterns - Theory and Applications. - Jens Auer; Martin Vogt 001; Jürgen Bajorath (Contrast Data Mining, 2013)

Systematic mining of analog series with related core structures in multi-target activity space. - Disha Gupta-Ostermann; Ye Hu; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2013)

Activity cliffs in PubChem confirmatory bioassays taking inactive compounds into account. - Ye Hu; Gerald M. Maggiora; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2013)

Statistical modeling of value distributions of similarity coefficients in virtual screening and its application to predicting fingerprint search performance. - Martin Vogt 001; Jürgen Bajorath (J. Cheminformatics, 2013)

Predicting Potent Compounds via Model-Based Global Optimization. - Mohsen Ahmadi; Martin Vogt 001; Preeti Iyer; Jürgen Bajorath; Holger Fröhlich (J. Chem. Inf. Model., 2013)

Searching for Closely Related Ligands with Different Mechanisms of Action Using Machine Learning and Mapping Algorithms. - Jenny Balfer; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Quantifying the Fingerprint Descriptor Dependence of Structure-Activity Relationship Information on a Large Scale. - Dilyana Dimova; Dagmar Stumpfe; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Prediction of Compounds with Closely Related Activity Profiles Using Weighted Support Vector Machine Linear Combinations. - Kathrin Heikamp; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Comparison of Confirmed Inactive and Randomly Selected Compounds as Negative Training Examples in Support Vector Machine-Based Virtual Screening. - Kathrin Heikamp; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Systematic Identification of Scaffolds Representing Compounds Active against Individual Targets and Single or Multiple Target Families. - Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Introduction of Target Cliffs as a Concept To Identify and Describe Complex Molecular Selectivity Patterns. - Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Compound Optimization through Data Set-Dependent Chemical Transformations. - Antonio de la Vega de León; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Classification of Compounds with Distinct or Overlapping Multi-Target Activities and Diverse Molecular Mechanisms Using Emerging Chemical Patterns. - Vigneshwaran Namasivayam; Ye Hu; Jenny Balfer; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Prediction of Individual Compounds Forming Activity Cliffs Using Emerging Chemical Patterns. - Vigneshwaran Namasivayam; Preeti Iyer; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Compound Pathway Model To Capture SAR Progression: Comparison of Activity Cliff-Dependent and -Independent Pathways. - Dagmar Stumpfe; Dilyana Dimova; Kathrin Heikamp; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Similarity Searching for Potent Compounds Using Feature Selection. - Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Conditional Probabilities of Activity Landscape Features for Individual Compounds. - Martin Vogt 001; Preeti Iyer; Gerald M. Maggiora; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

SAR Transfer across Different Targets. - Bijun Zhang; Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2013)

Compound data sets and software tools for chemoinformatics and medicinal chemistry applications: update and data transfer. - Ye Hu; Jürgen Bajorath (F1000Research, 2014)

Chemical space networks: a powerful new paradigm for the description of chemical space. - Gerald M. Maggiora; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2014)

Design of an activity landscape view taking compound-based feature probabilities into account. - Bijun Zhang; Martin Vogt 001; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2014)

Evaluation of molecular model-based discovery of ecto-5'-nucleotidase inhibitors on the basis of X-ray structures. - Norbert Furtmann; Jürgen Bajorath (J. Cheminformatics, 2014)

Introduction of a Methodology for Visualization and Graphical Interpretation of Bayesian Classification Models. - Jenny Balfer; Jürgen Bajorath (J. Chem. Inf. Model., 2014)

Neighborhood-Based Prediction of Novel Active Compounds from SAR Matrices. - Disha Gupta-Ostermann; Veerabahu Shanmugasundaram; Jürgen Bajorath (J. Chem. Inf. Model., 2014)

Influence of Search Parameters and Criteria on Compound Selection, Promiscuity, and Pan Assay Interference Characteristics. - Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2014)

Large-Scale Assessment of Activity Landscape Feature Probabilities of Bioactive Compounds. - Shilva Kayastha; Dilyana Dimova; Preeti Iyer; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2014)

Prediction of Compound Potency Changes in Matched Molecular Pairs Using Support Vector Regression. - Antonio de la Vega de León; Jürgen Bajorath (J. Chem. Inf. Model., 2014)

Prediction of Compounds in Different Local Structure-Activity Relationship Environments Using Emerging Chemical Patterns. - Vigneshwaran Namasivayam; Disha Gupta-Ostermann; Jenny Balfer; Kathrin Heikamp; Jürgen Bajorath (J. Chem. Inf. Model., 2014)

Composition and Topology of Activity Cliff Clusters Formed by Bioactive Compounds. - Dagmar Stumpfe; Dilyana Dimova; Jürgen Bajorath (J. Chem. Inf. Model., 2014)

Follow-up: Prospective compound design using the 'SAR Matrix' method and matrix-derived conditional probabilities of activity. - Disha Gupta-Ostermann; Yoichiro Hirose; Takenao Odagami; Hiroyuki Kouji; Jürgen Bajorath (F1000Research, 2015)

Comprehensive knowledge base of two- and three-dimensional activity cliffs for medicinal and computational chemistry. - Ye Hu; Norbert Furtmann; Dagmar Stumpfe; Jürgen Bajorath (F1000Research, 2015)

AnalogExplorer2 - Stereochemistry sensitive graphical analysis of large analog series. - Ye Hu; Bijun Zhang; Martin Vogt 001; Jürgen Bajorath (F1000Research, 2015)

Introducing the 'active search' method for iterative virtual screening. - Roman Garnett; Thomas Gärtner 001; Martin Vogt 001; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2015)

Visualization of multi-property landscapes for compound selection and optimization. - Antonio de la Vega de León; Shilva Kayastha; Dilyana Dimova; Thomas Schultz 001; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2015)

Comparison of bioactive chemical space networks generated using substructure- and fingerprint-based measures of molecular similarity. - Bijun Zhang; Martin Vogt 001; Gerald M. Maggiora; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2015)

Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures. - Bijun Zhang; Martin Vogt 001; Gerald M. Maggiora; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2015)

Erratum to: Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures. - Bijun Zhang; Martin Vogt 001; Gerald M. Maggiora; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2015)

Design and characterization of chemical space networks for different compound data sets. - Magdalena Zwierzyna; Martin Vogt 001; Gerald M. Maggiora; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2015)

Computational Polypharmacology Analysis of the Heat Shock Protein 90 Interactome. - Andrew Anighoro; Dagmar Stumpfe; Kathrin Heikamp; Kristin Beebe; Leonard M. Neckers; Jürgen Bajorath; Giulio Rastelli (J. Chem. Inf. Model., 2015)

Visualization and Interpretation of Support Vector Machine Activity Predictions. - Jenny Balfer; Jürgen Bajorath (J. Chem. Inf. Model., 2015)

Analyzing compound activity records and promiscuity degrees in light of publication statistics. - Ye Hu; Jürgen Bajorath (F1000Research, 2016)

Activity-relevant similarity values for fingerprints and implications for similarity searching. - Swarit Jasial; Ye Hu; Martin Vogt 001; Jürgen Bajorath (F1000Research, 2016)

Design of chemical space networks incorporating compound distance relationships. - Antonio de la Vega de León; Jürgen Bajorath (F1000Research, 2016)

Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A2A receptor. - Andrew Anighoro; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2016)

Predicting bioactive conformations and binding modes of macrocycles. - Andrew Anighoro; Antonio de la Vega de León; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2016)

Maximum common substructure-based Tversky index: an asymmetric hybrid similarity measure. - Ryo Kunimoto; Martin Vogt 001; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2016)

Lessons learned from the design of chemical space networks and opportunities for new applications. - Martin Vogt 001; Dagmar Stumpfe; Gerald M. Maggiora; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2016)

Design of chemical space networks on the basis of Tversky similarity. - Mengjun Wu; Martin Vogt 001; Gerald M. Maggiora; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2016)

Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes. - Andrew Anighoro; Jürgen Bajorath (J. Chem. Inf. Model., 2016)

Prediction of Activity Cliffs Using Condensed Graphs of Reaction Representations, Descriptor Recombination, Support Vector Machine Classification, and Support Vector Regression. - Dragos Horvath; Gilles Marcou; Alexandre Varnek; Shilva Kayastha; Antonio de la Vega de León; Jürgen Bajorath (J. Chem. Inf. Model., 2016)

Assessing the Growth of Bioactive Compounds and Scaffolds over Time: Implications for Lead Discovery and Scaffold Hopping. - Swarit Jasial; Ye Hu; Jürgen Bajorath (J. Chem. Inf. Model., 2016)

Application of generative autoencoder in de novo molecular design. - Thomas Blaschke; Marcus Olivecrona; Ola Engkvist; Jürgen Bajorath; Hongming Chen 001 (CoRR, 2017)

Expanding the chemical information science gateway. - Jürgen Bajorath (F1000Research, 2017)

Exploring differential evolution for inverse QSAR analysis. - Tomoyuki Miyao; Kimito Funatsu; Jürgen Bajorath (F1000Research, 2017)

Is scaffold hopping a reliable indicator for the ability of computational methods to identify structurally diverse active compounds? - Dilyana Dimova; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2017)

From bird's eye views to molecular communities: two-layered visualization of structure-activity relationships in large compound data sets. - Shilva Kayastha; Ryo Kunimoto; Dragos Horvath; Alexandre Varnek; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2017)

Exploring sets of molecules from patents and relationships to other active compounds in chemical space networks. - Ryo Kunimoto; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2017)

Privileged Structural Motif Detection and Analysis Using Generative Topographic Maps. - Shilva Kayastha; Dragos Horvath; Erik Gilberg; Michael Gütschow; Jürgen Bajorath; Alexandre Varnek (J. Chem. Inf. Model., 2017)

Influence of Varying Training Set Composition and Size on Support Vector Machine-Based Prediction of Active Compounds. - Raquel Rodríguez-Pérez; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2017)

Collection of analog series-based (ASB) scaffolds shared between ZINC, ChEMBL, and PubChem. - Carmen Cerchia; Dilyana Dimova; Antonio Lavecchia; Jürgen Bajorath (Zenodo, 2017)

Collection of analog series-based (ASB) scaffolds. - Dilyana Dimova; Jürgen Bajorath (Zenodo, 2017)

Analog Series of Compounds with High Frequency of Activity in Screening Assays. - Erik Gilberg; Dagmar Stumpfe; Jürgen Bajorath (Zenodo, 2017)

Analog Series of Compounds with High Frequency of Activity in Screening Assays. - Dagmar Stumpfe; Erik Gilberg; Jürgen Bajorath (Zenodo, 2017)

Compounds with multi-target activity from X-ray structures, corresponding analog series, and associated scaffolds. - Erik Gilberg; Dagmar Stumpfe; Jürgen Bajorath (Zenodo, 2017)

Design of a tripartite network for the prediction of drug targets. - Ryo Kunimoto; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2018)

Exploring ensembles of bioactive or virtual analogs of X-ray ligands for shape similarity searching. - Tomoyuki Miyao; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2018)

X-Ray Structures of Target-Ligand Complexes Containing Compounds with Assay Interference Potential. - Erik Gilberg; Michael Gütschow; Jürgen Bajorath (Zenodo, 2018)

X-Ray Structures of Target-Ligand Complexes Containing Compounds with Assay Interference Potential. - Erik Gilberg; Michael Gütschow; Jürgen Bajorath (Zenodo, 2018)

Target set-dependent activity cliffs. - Huabin Hu; Dagmar Stumpfe; Jürgen Bajorath (Zenodo, 2018)

Repositioning the Chemical Information Science Gateway. - Jürgen Bajorath (F1000Research, 2019)

Systematic computational identification of promiscuity cliff pathways formed by inhibitors of the human kinome. - Filip Miljkovic; Martin Vogt 001; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2019)

Evaluation of different virtual screening strategies on the basis of compound sets with characteristic core distributions and dissimilarity relationships. - Tomoyuki Miyao; Swarit Jasial; Jürgen Bajorath; Kimito Funatsu (J. Comput. Aided Mol. Des., 2019)

Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold hopping capability. - Oliver Laufkötter; Noé Sturm; Jürgen Bajorath; Hongming Chen 001; Ola Engkvist (J. Cheminformatics, 2019)

A general approach for retrosynthetic molecular core analysis. - J. Jesús Naveja; B. Angélica Pilón-Jiménez; Jürgen Bajorath; José L. Medina-Franco (J. Cheminformatics, 2019)

Virtual Screening with Generative Topographic Maps: How Many Maps Are Required? - Iuri Casciuc; Yuliana Zabolotna; Dragos Horvath; Gilles Marcou; Jürgen Bajorath; Alexandre Varnek (J. Chem. Inf. Model., 2019)

Exploring Alternative Strategies for the Identification of Potent Compounds Using Support Vector Machine and Regression Modeling. - Tomoyuki Miyao; Kimito Funatsu; Jürgen Bajorath (J. Chem. Inf. Model., 2019)

Three-Dimensional Activity Landscape Models of Different Design and Their Application to Compound Mapping and Potency Prediction. - Tomoyuki Miyao; Kimito Funatsu; Jürgen Bajorath (J. Chem. Inf. Model., 2019)

Exploration of Target Synergy in Cancer Treatment by Cell-Based Screening Assay and Network Propagation Analysis. - J. Jesús Naveja; Dagmar Stumpfe; José L. Medina-Franco; Jürgen Bajorath (J. Chem. Inf. Model., 2019)

Method for Systematic Analogue Search Using the Mega SAR Matrix Database. - Atsushi Yoshimori; Yuichi Horita; Toru Tanoue; Jürgen Bajorath (J. Chem. Inf. Model., 2019)

Promiscuity cliffs (PCs), promiscuity cliff pathways (PCPs), and promiscuity hubs (PHs) formed by inhibitors of human kinases. - Filip Miljkovic; Jürgen Bajorath (Zenodo, 2019)

Machine Learning Models for Predicting Kinase Inhibitors with Different Binding Modes. - Filip Miljkovic; Raquel Rodríguez-Pérez; Jürgen Bajorath (Zenodo, 2019)

Machine Learning Models for Predicting Kinase Inhibitors with Different Binding Modes. - Filip Miljkovic; Raquel Rodríguez-Pérez; Jürgen Bajorath (Zenodo, 2019)

Compound activity classes from ChEMBL for machine learning analysis. - Raquel Rodríguez-Pérez; Jürgen Bajorath (Zenodo, 2019)

Compound activity classes from ChEMBL for machine learning analysis. - Raquel Rodríguez-Pérez; Jürgen Bajorath (Zenodo, 2019)

Promiscuous compounds with activity against different target classes. - Christian Feldmann; Filip Miljkovic; Dimitar G. Yonchev; Jürgen Bajorath (Zenodo, 2019)

ccbmlib - a Python package for modeling Tanimoto similarity value distributions. - Martin Vogt 001; Jürgen Bajorath (F1000Research, 2020)

Simplified activity cliff network representations with high interpretability and immediate access to SAR information. - Huabin Hu; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2020)

Data structures for computational compound promiscuity analysis and exemplary applications to inhibitors of the human kinome. - Filip Miljkovic; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2020)

Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions. - Raquel Rodríguez-Pérez; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2020)

Advances in exploring activity cliffs. - Dagmar Stumpfe; Huabin Hu; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2020)

DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology. - Dimitar G. Yonchev; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2020)

Activity landscape image analysis using convolutional neural networks. - Javed Iqbal; Martin Vogt 001; Jürgen Bajorath (J. Cheminformatics, 2020)

Assessing the information content of structural and protein-ligand interaction representations for the classification of kinase inhibitor binding modes via machine learning and active learning. - Raquel Rodríguez-Pérez; Filip Miljkovic; Jürgen Bajorath (J. Cheminformatics, 2020)

From Qualitative to Quantitative Analysis of Activity and Property Landscapes. - Gerald M. Maggiora; José L. Medina-Franco; Javed Iqbal; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2020)

Current Trends, Overlooked Issues, and Unmet Challenges in Virtual Screening. - Dagmar Stumpfe; Jürgen Bajorath (J. Chem. Inf. Model., 2020)

ccbmlib - a Python Package for Modeling Tanimoto Coefficient Distributions for Molecular Fingerprints. - Martin Vogt 001; Jürgen Bajorath (Zenodo, 2020)

ccbmlib - a Python Package for Modeling Tanimoto Coefficient Distributions for Molecular Fingerprints. - Martin Vogt 001; Jürgen Bajorath (Zenodo, 2020)

Systematic Data Analysis and Diagnostic Machine Learning Reveal Differences between Compounds with Single- and Multitarget Activity. - Christian Feldmann; Dimitar G. Yonchev; Dagmar Stumpfe; Jürgen Bajorath (Zenodo, 2020)

Substituents isolated from analog series. - Kosuke Takeuchi; Ryo Kunimoto; Jürgen Bajorath (Zenodo, 2020)

Data sets for compound promiscuity analysis and predictions. - Christian Feldmann; Dimitar G. Yonchev; Jürgen Bajorath (Zenodo, 2020)

Rationality over fashion and hype in drug design. - José L. Medina-Franco; Karina Martínez-Mayorga; Eli Fernández-de Gortari; Johannes Kirchmair; Jürgen Bajorath (F1000Research, 2021)

Prediction of activity cliffs on the basis of images using convolutional neural networks. - Javed Iqbal; Martin Vogt 001; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2021)

Evaluation of multi-target deep neural network models for compound potency prediction under increasingly challenging test conditions. - Raquel Rodríguez-Pérez; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2021)

Adapting the DeepSARM approach for dual-target ligand design. - Atsushi Yoshimori; Huabin Hu; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2021)

Informatics for Chemistry, Biology, and Biomedical Sciences. - Edgar López-López; Jürgen Bajorath; José L. Medina-Franco (J. Chem. Inf. Model., 2021)

Metacores. - Dagmar Stumpfe; Alexander Hoch; Jürgen Bajorath (Zenodo, 2021)

Fine-tuning of a generative neural network for designing multi-target compounds. - Thomas Blaschke; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2022)

Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery. - Raquel Rodríguez-Pérez; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2022)

Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor, colleague, collaborator, and innovator. - Veerabahu Shanmugasundaram; Jürgen Bajorath; Ralph E. Christoffersen; James D. Petke; W. Jeffrey Howe; Mark A. Johnson; Dimitris K. Agrafiotis; Pil Lee; Leslie A. Kuhn; Jay T. Goodwin; M. Katharine Holloway; Thompson N. Doman; et al. (J. Comput. Aided Mol. Des., 2022)

Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds. - Jürgen Bajorath; Ana L. Chávez-Hernández; Miquel Duran-Frigola; Eli Fernández-de Gortari; Johann Gasteiger; Edgar López-López; Gerald M. Maggiora; José L. Medina-Franco; Oscar Méndez-Lucio; Jordi Mestres; Ramón Alain Miranda-Quintana; Tudor I. Oprea; et al. (J. Cheminformatics, 2022)

Candidate compounds from the design of covalent Bruton's tyrosine kinase (BTK) inhibitors via focused deep generative modeling. - Atsushi Yoshimori; Filip Miljkovic; Jürgen Bajorath (Zenodo, 2022)

Calculation of Exact Shapley Values for Support Vector Machines with Tanimoto Kernel Enables Model Interpretation. - Christian Feldmann; Jürgen Bajorath (Zenodo, 2022)

Calculation of Exact Shapley Values for Support Vector Machines with Tanimoto Kernel Enables Model Interpretation. - Christian Feldmann; Jürgen Bajorath (Zenodo, 2022)

DeepAC - Conditional transformer-based chemical language model for the prediction of activity cliffs formed by bioactive compounds. - Hengwei Chen; Martin Vogt 001; Jürgen Bajorath (Zenodo, 2022)

Minimal Data Requirements for Accurate Compound Activity Prediction Using Machine Learning Methods of Different Complexity. - Friederike Maite Siemers; Christian Feldmann; Jürgen Bajorath (Zenodo, 2022)

Simple nearest-neighbour analysis meets the accuracy of compound potency predictions using complex machine learning models. - Tiago Janela; Jürgen Bajorath (Nat. Mac. Intell., 2022)

Large-scale prediction of activity cliffs using machine and deep learning methods of increasing complexity. - Shunsuke Tamura; Tomoyuki Miyao; Jürgen Bajorath (J. Cheminformatics, 2023)

DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds. - Kohei Umedera; Atsushi Yoshimori; Hengwei Chen; Hiroyuki Kouji; Hiroyuki Nakamura; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2023)

Designing highly potent compounds using a chemical language model. - Hengwei Chen; Jürgen Bajorath (Zenodo, 2023)

Protein kinase inhibitors. - Elena Xerxa; Filip Miljkovic; Jürgen Bajorath (Zenodo, 2023)

Allosteric kinase inhibitors. - Elena Xerxa; Oliver Laufkötter; Jürgen Bajorath (Zenodo, 2023)

CIRCE: Web-Based Platform for the Prediction of Cannabinoid Receptor Ligands Using Explainable Machine Learning. - Nicola Gambacorta; Fulvio Ciriaco; Nicola Amoroso; Cosimo Damiano Altomare; Jürgen Bajorath; Orazio Nicolotti (J. Chem. Inf. Model., 2023)

Anatomy of Potency Predictions Focusing on Structural Analogues with Increasing Potency Differences Including Activity Cliffs. - Tiago Janela; Jürgen Bajorath (J. Chem. Inf. Model., 2023)

Learning characteristics of graph neural networks predicting protein-ligand affinities. - Andrea Mastropietro; Giuseppe Pasculli; Jürgen Bajorath (Nat. Mac. Intell., 2023)

Combining a Chemical Language Model and the Structure-Activity Relationship Matrix Formalism for Generative Design of Potent Compounds with Core Structure and Substituent Modifications. - Hengwei Chen; Jürgen Bajorath (J. Chem. Inf. Model., 2024)

Influence of Data Curation and Confidence Levels on Compound Predictions Using Machine Learning Models. - Elena Xerxa; Martin Vogt 001; Jürgen Bajorath (J. Chem. Inf. Model., 2024)

Code for: Relationship between prediction accuracy and uncertainty in compound potency prediction using deep neural networks and control models. - Jannik Philipp Roth; Jürgen Bajorath (Zenodo, 2024)

Code for: Alternative Kernel Functions in Support Vector Machine Models Lead to Distinct Shapley Value Explanations of Compound Predictions that Decouple Feature Attribution and Model Interpretation. - Jannik Philipp Roth; Jürgen Bajorath (Zenodo, 2024)

Milestones in chemoinformatics: global view of the field. - Jürgen Bajorath (J. Cheminformatics, 2024)

Generative design of compounds with desired potency from target protein sequences using a multimodal biochemical language model. - Hengwei Chen; Jürgen Bajorath (J. Cheminformatics, 2024)

Rationalizing Predictions of Isoform-Selective Phosphoinositide 3-Kinase Inhibitors Using MolAnchor Analysis. - Alec Lamens; Jürgen Bajorath (J. Chem. Inf. Model., 2025)

Context-dependent similarity analysis of analogue series for structure-activity relationship transfer based on a concept from natural language processing. - Atsushi Yoshimori; Jürgen Bajorath (J. Cheminformatics, 2025)

Context-dependent similarity searching for small molecular fragments. - Atsushi Yoshimori; Jürgen Bajorath (J. Cheminformatics, 2025)