Jürgen Bajorath

Orcid: 0000-0002-0557-5714

Affiliations:
  • University of Bonn, Germany


According to our database1, Jürgen Bajorath authored at least 209 papers between 1997 and 2023.

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Bibliography

2023
Learning characteristics of graph neural networks predicting protein-ligand affinities.
Nat. Mac. Intell., December, 2023

Anatomy of Potency Predictions Focusing on Structural Analogues with Increasing Potency Differences Including Activity Cliffs.
J. Chem. Inf. Model., November, 2023

CIRCE: Web-Based Platform for the Prediction of Cannabinoid Receptor Ligands Using Explainable Machine Learning.
J. Chem. Inf. Model., September, 2023

DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds.
J. Comput. Aided Mol. Des., February, 2023

Large-scale prediction of activity cliffs using machine and deep learning methods of increasing complexity.
J. Cheminformatics, 2023

2022
Simple nearest-neighbour analysis meets the accuracy of compound potency predictions using complex machine learning models.
Nat. Mac. Intell., December, 2022

Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds.
J. Cheminformatics, 2022

Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor, colleague, collaborator, and innovator.
J. Comput. Aided Mol. Des., 2022

Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery.
J. Comput. Aided Mol. Des., 2022

Fine-tuning of a generative neural network for designing multi-target compounds.
J. Comput. Aided Mol. Des., 2022

2021
Informatics for Chemistry, Biology, and Biomedical Sciences.
J. Chem. Inf. Model., 2021

Adapting the DeepSARM approach for dual-target ligand design.
J. Comput. Aided Mol. Des., 2021

Evaluation of multi-target deep neural network models for compound potency prediction under increasingly challenging test conditions.
J. Comput. Aided Mol. Des., 2021

Prediction of activity cliffs on the basis of images using convolutional neural networks.
J. Comput. Aided Mol. Des., 2021

Rationality over fashion and hype in drug design.
F1000Research, 2021

2020
Current Trends, Overlooked Issues, and Unmet Challenges in Virtual Screening.
J. Chem. Inf. Model., 2020

From Qualitative to Quantitative Analysis of Activity and Property Landscapes.
J. Chem. Inf. Model., 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.
J. Cheminformatics, 2020

Activity landscape image analysis using convolutional neural networks.
J. Cheminformatics, 2020

DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology.
J. Comput. Aided Mol. Des., 2020

Advances in exploring activity cliffs.
J. Comput. Aided Mol. Des., 2020

Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions.
J. Comput. Aided Mol. Des., 2020

Data structures for computational compound promiscuity analysis and exemplary applications to inhibitors of the human kinome.
J. Comput. Aided Mol. Des., 2020

Simplified activity cliff network representations with high interpretability and immediate access to SAR information.
J. Comput. Aided Mol. Des., 2020

ccbmlib - a Python package for modeling Tanimoto similarity value distributions.
F1000Research, 2020

2019
Method for Systematic Analogue Search Using the Mega SAR Matrix Database.
J. Chem. Inf. Model., 2019

Exploration of Target Synergy in Cancer Treatment by Cell-Based Screening Assay and Network Propagation Analysis.
J. Chem. Inf. Model., 2019

Three-Dimensional Activity Landscape Models of Different Design and Their Application to Compound Mapping and Potency Prediction.
J. Chem. Inf. Model., 2019

Exploring Alternative Strategies for the Identification of Potent Compounds Using Support Vector Machine and Regression Modeling.
J. Chem. Inf. Model., 2019

Virtual Screening with Generative Topographic Maps: How Many Maps Are Required?
J. Chem. Inf. Model., 2019

A general approach for retrosynthetic molecular core analysis.
J. Cheminformatics, 2019

Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold hopping capability.
J. Cheminformatics, 2019

Evaluation of different virtual screening strategies on the basis of compound sets with characteristic core distributions and dissimilarity relationships.
J. Comput. Aided Mol. Des., 2019

Systematic computational identification of promiscuity cliff pathways formed by inhibitors of the human kinome.
J. Comput. Aided Mol. Des., 2019

Repositioning the Chemical Information Science Gateway.
F1000Research, 2019

2018
Exploring ensembles of bioactive or virtual analogs of X-ray ligands for shape similarity searching.
J. Comput. Aided Mol. Des., 2018

Design of a tripartite network for the prediction of drug targets.
J. Comput. Aided Mol. Des., 2018

2017
Influence of Varying Training Set Composition and Size on Support Vector Machine-Based Prediction of Active Compounds.
J. Chem. Inf. Model., 2017

Privileged Structural Motif Detection and Analysis Using Generative Topographic Maps.
J. Chem. Inf. Model., 2017

Exploring sets of molecules from patents and relationships to other active compounds in chemical space networks.
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.
J. Comput. Aided Mol. Des., 2017

Is scaffold hopping a reliable indicator for the ability of computational methods to identify structurally diverse active compounds?
J. Comput. Aided Mol. Des., 2017

Exploring differential evolution for inverse QSAR analysis.
F1000Research, 2017

Expanding the chemical information science gateway.
F1000Research, 2017

Application of generative autoencoder in de novo molecular design.
CoRR, 2017

2016
Assessing the Growth of Bioactive Compounds and Scaffolds over Time: Implications for Lead Discovery and Scaffold Hopping.
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.
J. Chem. Inf. Model., 2016

Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes.
J. Chem. Inf. Model., 2016

Design of chemical space networks on the basis of Tversky similarity.
J. Comput. Aided Mol. Des., 2016

Lessons learned from the design of chemical space networks and opportunities for new applications.
J. Comput. Aided Mol. Des., 2016

Maximum common substructure-based Tversky index: an asymmetric hybrid similarity measure.
J. Comput. Aided Mol. Des., 2016

Predicting bioactive conformations and binding modes of macrocycles.
J. Comput. Aided Mol. Des., 2016

Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A2A receptor.
J. Comput. Aided Mol. Des., 2016

Design of chemical space networks incorporating compound distance relationships.
F1000Research, 2016

Activity-relevant similarity values for fingerprints and implications for similarity searching.
F1000Research, 2016

Analyzing compound activity records and promiscuity degrees in light of publication statistics.
F1000Research, 2016

2015
Visualization and Interpretation of Support Vector Machine Activity Predictions.
J. Chem. Inf. Model., 2015

Computational Polypharmacology Analysis of the Heat Shock Protein 90 Interactome.
J. Chem. Inf. Model., 2015

Design and characterization of chemical space networks for different compound data sets.
J. Comput. Aided Mol. Des., 2015

Erratum to: Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures.
J. Comput. Aided Mol. Des., 2015

Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures.
J. Comput. Aided Mol. Des., 2015

Comparison of bioactive chemical space networks generated using substructure- and fingerprint-based measures of molecular similarity.
J. Comput. Aided Mol. Des., 2015

Visualization of multi-property landscapes for compound selection and optimization.
J. Comput. Aided Mol. Des., 2015

Introducing the 'active search' method for iterative virtual screening.
J. Comput. Aided Mol. Des., 2015

AnalogExplorer2 - Stereochemistry sensitive graphical analysis of large analog series.
F1000Research, 2015

Comprehensive knowledge base of two- and three-dimensional activity cliffs for medicinal and computational chemistry.
F1000Research, 2015

Follow-up: Prospective compound design using the 'SAR Matrix' method and matrix-derived conditional probabilities of activity.
F1000Research, 2015

2014
Composition and Topology of Activity Cliff Clusters Formed by Bioactive Compounds.
J. Chem. Inf. Model., 2014

Prediction of Compounds in Different Local Structure-Activity Relationship Environments Using Emerging Chemical Patterns.
J. Chem. Inf. Model., 2014

Prediction of Compound Potency Changes in Matched Molecular Pairs Using Support Vector Regression.
J. Chem. Inf. Model., 2014

Large-Scale Assessment of Activity Landscape Feature Probabilities of Bioactive Compounds.
J. Chem. Inf. Model., 2014

Influence of Search Parameters and Criteria on Compound Selection, Promiscuity, and Pan Assay Interference Characteristics.
J. Chem. Inf. Model., 2014

Neighborhood-Based Prediction of Novel Active Compounds from SAR Matrices.
J. Chem. Inf. Model., 2014

Introduction of a Methodology for Visualization and Graphical Interpretation of Bayesian Classification Models.
J. Chem. Inf. Model., 2014

Evaluation of molecular model-based discovery of ecto-5'-nucleotidase inhibitors on the basis of X-ray structures.
J. Cheminformatics, 2014

Design of an activity landscape view taking compound-based feature probabilities into account.
J. Comput. Aided Mol. Des., 2014

Chemical space networks: a powerful new paradigm for the description of chemical space.
J. Comput. Aided Mol. Des., 2014

Compound data sets and software tools for chemoinformatics and medicinal chemistry applications: update and data transfer.
F1000Research, 2014

2013
SAR Transfer across Different Targets.
J. Chem. Inf. Model., 2013

Conditional Probabilities of Activity Landscape Features for Individual Compounds.
J. Chem. Inf. Model., 2013

Similarity Searching for Potent Compounds Using Feature Selection.
J. Chem. Inf. Model., 2013

Compound Pathway Model To Capture SAR Progression: Comparison of Activity Cliff-Dependent and -Independent Pathways.
J. Chem. Inf. Model., 2013

Prediction of Individual Compounds Forming Activity Cliffs Using Emerging Chemical Patterns.
J. Chem. Inf. Model., 2013

Classification of Compounds with Distinct or Overlapping Multi-Target Activities and Diverse Molecular Mechanisms Using Emerging Chemical Patterns.
J. Chem. Inf. Model., 2013

Compound Optimization through Data Set-Dependent Chemical Transformations.
J. Chem. Inf. Model., 2013

Introduction of Target Cliffs as a Concept To Identify and Describe Complex Molecular Selectivity Patterns.
J. Chem. Inf. Model., 2013

Systematic Identification of Scaffolds Representing Compounds Active against Individual Targets and Single or Multiple Target Families.
J. Chem. Inf. Model., 2013

Comparison of Confirmed Inactive and Randomly Selected Compounds as Negative Training Examples in Support Vector Machine-Based Virtual Screening.
J. Chem. Inf. Model., 2013

Prediction of Compounds with Closely Related Activity Profiles Using Weighted Support Vector Machine Linear Combinations.
J. Chem. Inf. Model., 2013

Quantifying the Fingerprint Descriptor Dependence of Structure-Activity Relationship Information on a Large Scale.
J. Chem. Inf. Model., 2013

Searching for Closely Related Ligands with Different Mechanisms of Action Using Machine Learning and Mapping Algorithms.
J. Chem. Inf. Model., 2013

Predicting Potent Compounds via Model-Based Global Optimization.
J. Chem. Inf. Model., 2013

Statistical modeling of value distributions of similarity coefficients in virtual screening and its application to predicting fingerprint search performance.
J. Cheminformatics, 2013

Activity cliffs in PubChem confirmatory bioassays taking inactive compounds into account.
J. Comput. Aided Mol. Des., 2013

Systematic mining of analog series with related core structures in multi-target activity space.
J. Comput. Aided Mol. Des., 2013

Emerging Chemical Patterns - Theory and Applications.
Proceedings of the Contrast Data Mining: Concepts, Algorithms, and Applications, 2013

2012
Systematic Assessment of Compound Series with SAR Transfer Potential.
J. Chem. Inf. Model., 2012

SAR Matrices: Automated Extraction of Information-Rich SAR Tables from Large Compound Data Sets.
J. Chem. Inf. Model., 2012

Frequency of Occurrence and Potency Range Distribution of Activity Cliffs in Bioactive Compounds.
J. Chem. Inf. Model., 2012

Multiobjective Particle Swarm Optimization: Automated Identification of Structure-Activity Relationship-Informative Compounds with Favorable Physicochemical Property Distributions.
J. Chem. Inf. Model., 2012

Searching for Coordinated Activity Cliffs Using Particle Swarm Optimization.
J. Chem. Inf. Model., 2012

Design of a Three-Dimensional Multitarget Activity Landscape.
J. Chem. Inf. Model., 2012

Navigating High-Dimensional Activity Landscapes: Design and Application of the Ligand-Target Differentiation Map.
J. Chem. Inf. Model., 2012

MMP-Cliffs: Systematic Identification of Activity Cliffs on the Basis of Matched Molecular Pairs.
J. Chem. Inf. Model., 2012

Systematic Identification and Classification of Three-Dimensional Activity Cliffs.
J. Chem. Inf. Model., 2012

Growth of Ligand-Target Interaction Data in ChEMBL Is Associated with Increasing and Activity Measurement-Dependent Compound Promiscuity.
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.
J. Chem. Inf. Model., 2012

Exploration of 3D Activity Cliffs on the Basis of Compound Binding Modes and Comparison of 2D and 3D Cliffs.
J. Chem. Inf. Model., 2012

Prediction of Activity Cliffs Using Support Vector Machines.
J. Chem. Inf. Model., 2012

Graph Mining for SAR Transfer Series.
J. Chem. Inf. Model., 2012

Identification of Multitarget Activity Ridges in High-Dimensional Bioactivity Spaces.
J. Chem. Inf. Model., 2012

A computational method to facilitate structure-activity relationship transfer.
J. Cheminformatics, 2012

Potency-directed similarity searching using support vector machines.
J. Cheminformatics, 2012

Design of multi-target activity landscapes that capture hierarchical activity cliff distributions.
J. Cheminformatics, 2012

Systematic assessment of scaffold distances in ChEMBL: prioritization of compound data sets for scaffold hopping analysis in virtual screening.
J. Comput. Aided Mol. Des., 2012

Computational chemistry in pharmaceutical research: at the crossroads.
J. Comput. Aided Mol. Des., 2012

Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications.
F1000Research, 2012

2011
Correction to Identification of Descriptors Capturing Compound Class-Specific Features by Mutual Information Analysis.
J. Chem. Inf. Model., 2011

A Data Mining Method To Facilitate SAR Transfer.
J. Chem. Inf. Model., 2011

From Activity Cliffs to Activity Ridges: Informative Data Structures for SAR Analysis.
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.
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.
J. Chem. Inf. Model., 2011

REPROVIS-DB: A Benchmark System for Ligand-Based Virtual Screening Derived from Reproducible Prospective Applications.
J. Chem. Inf. Model., 2011

Rationalizing the Role of SAR Tolerance for Ligand-Based Virtual Screening.
J. Chem. Inf. Model., 2011

Extraction of Discontinuous Structure-Activity Relationships from Compound Data Sets through Particle Swarm Optimization.
J. Chem. Inf. Model., 2011

Development of a Method To Consistently Quantify the Structural Distance between Scaffolds and To Assess Scaffold Hopping Potential.
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.
J. Chem. Inf. Model., 2011

SAR Monitoring of Evolving Compound Data Sets Using Activity Landscapes.
J. Chem. Inf. Model., 2011

Lessons Learned from Molecular Scaffold Analysis.
J. Chem. Inf. Model., 2011

Target Family-Directed Exploration of Scaffolds with Different SAR Profiles.
J. Chem. Inf. Model., 2011

Combining Horizontal and Vertical Substructure Relationships in Scaffold Hierarchies for Activity Prediction.
J. Chem. Inf. Model., 2011

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

Large-Scale Similarity Search Profiling of ChEMBL Compound Data Sets.
J. Chem. Inf. Model., 2011

Design of Multitarget Activity Landscapes That Capture Hierarchical Activity Cliff Distributions.
J. Chem. Inf. Model., 2011

2010
Similarity-Potency Trees: A Method to Search for SAR Information in Compound Data Sets and Derive SAR Rules.
J. Chem. Inf. Model., 2010

Identification of Descriptors Capturing Compound Class-Specific Features by Mutual Information Analysis.
J. Chem. Inf. Model., 2010

Chemical Substitutions That Introduce Activity Cliffs Across Different Compound Classes and Biological Targets.
J. Chem. Inf. Model., 2010

Rationalization of the Performance and Target Dependence of Similarity Searching Incorporating Protein-Ligand Interaction Information.
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.
J. Chem. Inf. Model., 2010

SARANEA: A Freely Available Program To Mine Structure-Activity and Structure-Selectivity Relationship Information in Compound Data Sets.
J. Chem. Inf. Model., 2010

Polypharmacology Directed Compound Data Mining: Identification of Promiscuous Chemotypes with Different Activity Profiles and Comparison to Approved Drugs.
J. Chem. Inf. Model., 2010

Molecular Scaffolds with High Propensity to Form Multi-Target Activity Cliffs.
J. Chem. Inf. Model., 2010

Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation.
J. Chem. Inf. Model., 2010

Atom-Centered Interacting Fragments and Similarity Search Applications.
J. Chem. Inf. Model., 2010

Design and Evaluation of Bonded Atom Pair Descriptors.
J. Chem. Inf. Model., 2010

Systematic extraction of structure-activity relationship information from biological screening data.
J. Cheminformatics, 2010

Adaptation of formal concept analysis for the systematic exploration of structure-activity and structure-selectivity relationships.
J. Cheminformatics, 2010

Application of Information - Theoretic Concepts in Chemoinformatics.
Inf., 2010

2009
Predicting the similarity search performance of fingerprints and their combination with molecular property descriptors using probabilistic and information theoretic modeling.
Stat. Anal. Data Min., 2009

Ligand Prediction for Orphan Targets Using Support Vector Machines and Various Target-Ligand Kernels Is Dominated by Nearest Neighbor Effects.
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.
J. Chem. Inf. Model., 2009

Shannon Entropy-Based Fingerprint Similarity Search Strategy.
J. Chem. Inf. Model., 2009

Development of a Compound Class-Directed Similarity Coefficient That Accounts for Molecular Complexity Effects in Fingerprint Searching.
J. Chem. Inf. Model., 2009

Structural Interpretation of Activity Cliffs Revealed by Systematic Analysis of Structure-Activity Relationships in Analog Series.
J. Chem. Inf. Model., 2009

Development of a Fingerprint Reduction Approach for Bayesian Similarity Searching Based on Kullback-Leibler Divergence Analysis.
J. Chem. Inf. Model., 2009

Molecular Formal Concept Analysis for Compound Selectivity Profiling in Biologically Annotated Databases.
J. Chem. Inf. Model., 2009

Relevance of Feature Combinations for Similarity Searching Using General or Activity Class-Directed Molecular Fingerprints.
J. Chem. Inf. Model., 2009

Topological Fragment Index for the Analysis of Molecular Substructures and Their Topological Environment in Active Compounds.
J. Chem. Inf. Model., 2009

Ligand Prediction from Protein Sequence and Small Molecule Information Using Support Vector Machines and Fingerprint Descriptors.
J. Chem. Inf. Model., 2009

2008
Bit Silencing in Fingerprints Enables the Derivation of Compound Class-Directed Similarity Metrics.
J. Chem. Inf. Model., 2008

Balancing the Influence of Molecular Complexity on Fingerprint Similarity Searching.
J. Chem. Inf. Model., 2008

Design and Exploration of Target-Selective Chemical Space Representations.
J. Chem. Inf. Model., 2008

Bayesian Similarity Searching in High-Dimensional Descriptor Spaces Combined with Kullback-Leibler Descriptor Divergence Analysis.
J. Chem. Inf. Model., 2008

Similarity Searching Using Fingerprints of Molecular Fragments Involved in Protein-Ligand Interactions.
J. Chem. Inf. Model., 2008

Core Trees and Consensus Fragment Sequences for Molecular Representation and Similarity Analysis.
J. Chem. Inf. Model., 2008

Support-Vector-Machine-Based Ranking Significantly Improves the Effectiveness of Similarity Searching Using 2D Fingerprints and Multiple Reference Compounds.
J. Chem. Inf. Model., 2008

Ligand-Target Interaction-Based Weighting of Substructures for Virtual Screening.
J. Chem. Inf. Model., 2008

Distinguishing between Bioactive and Modeled Compound Conformations through Mining of Emerging Chemical Patterns.
J. Chem. Inf. Model., 2008

2007
Bayesian Interpretation of a Distance Function for Navigating High-Dimensional Descriptor Spaces.
J. Chem. Inf. Model., 2007

Analysis of a High-Throughput Screening Data Set Using Potency-Scaled Molecular Similarity Algorithms.
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.
J. Chem. Inf. Model., 2007

Mapping of Activity-Specific Fragment Pathways Isolated from Random Fragment Populations Reveals the Formation of Coherent Molecular Cores.
J. Chem. Inf. Model., 2007

Exploring Peptide-likeness of Active Molecules Using 2D Fingerprint Methods.
J. Chem. Inf. Model., 2007

Mining of Randomly Generated Molecular Fragment Populations Uncovers Activity-Specific Fragment Hierarchies.
J. Chem. Inf. Model., 2007

Chemical Database Mining through Entropy-Based Molecular Similarity Assessment of Randomly Generated Structural Fragment Populations.
J. Chem. Inf. Model., 2007

2006
A Distance Function for Retrieval of Active Molecules from Complex Chemical Space Representations.
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.
J. Chem. Inf. Model., 2006

Design and Evaluation of a Novel Class-Directed 2D Fingerprint to Search for Structurally Diverse Active Compounds.
J. Chem. Inf. Model., 2006

Assessment of Molecular Similarity from the Analysis of Randomly Generated Structural Fragment Populations.
J. Chem. Inf. Model., 2006

Emerging Chemical Patterns: A New Methodology for Molecular Classification and Compound Selection.
J. Chem. Inf. Model., 2006

2005
Anatomy of Fingerprint Search Calculations on Structurally Diverse Sets of Active Compounds.
J. Chem. Inf. Model., 2005

2004
Similarity Search Profiling Reveals Effects of Fingerprint Scaling in Virtual Screening.
J. Chem. Inf. Model., 2004

Similarity Search Profiles as a Diagnostic Tool for the Analysis of Virtual Screening Calculations.
J. Chem. Inf. Model., 2004

Molecular Similarity Analysis and Virtual Screening by Mapping of Consensus Positions in Binary-Transformed Chemical Descriptor Spaces with Variable Dimensionality.
J. Chem. Inf. Model., 2004

2003
Profile Scaling Increases the Similarity Search Performance of Molecular Fingerprints Containing Numerical Descriptors and Structural Keys.
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.
J. Chem. Inf. Comput. Sci., 2003

Recursive Median Partitioning for Virtual Screening of Large Databases.
J. Chem. Inf. Comput. Sci., 2003

2002
Accurate Partitioning of Compounds Belonging to Diverse Activity Classes.
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.
J. Chem. Inf. Comput. Sci., 2002

Median Partitioning: A Novel Method for the Selection of Representative Subsets from Large Compound Pools.
J. Chem. Inf. Comput. Sci., 2002

Classification of Biologically Active Compounds by Median Partitioning.
J. Chem. Inf. Comput. Sci., 2002

Chemical Descriptors with Distinct Levels of Information Content and Varying Sensitivity to Differences between Selected Compound Databases Identified by SE-DSE Analysis.
J. Chem. Inf. Comput. Sci., 2002

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

2001
Fingerprint Scaling Increases the Probability of Identifying Molecules with Similar Activity in Virtual Screening Calculations.
J. Chem. Inf. Comput. Sci., 2001

Mini-fingerprints Detect Similar Activity of Receptor Ligands Previously Recognized Only by Three-Dimensional Pharmacophore-Based Methods.
J. Chem. Inf. Comput. Sci., 2001

Differential Shannon Entropy as a Sensitive Measure of Differences in Database Variability of Molecular Descriptors.
J. Chem. Inf. Comput. Sci., 2001

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

2000
Evaluation of Descriptors and Mini-Fingerprints for the Identification of Molecules with Similar Activity.
J. Chem. Inf. Comput. Sci., 2000

Distinguishing between Natural Products and Synthetic Molecules by Descriptor Shannon Entropy Analysis and Binary QSAR Calculations.
J. Chem. Inf. Comput. Sci., 2000

Combinatorial Preferences Affect Molecular Similarity/Diversity Calculations Using Binary Fingerprints and Tanimoto Coefficients.
J. Chem. Inf. Comput. Sci., 2000

Variability of Molecular Descriptors in Compound Databases Revealed by Shannon Entropy Calculations.
J. Chem. Inf. Comput. Sci., 2000

Molecular Descriptors for Effective Classification of Biologically Active Compounds Based on Principal Component Analysis Identified by a Genetic Algorithm.
J. Chem. Inf. Comput. Sci., 2000

1999
Identification of a Preferred Set of Molecular Descriptors for Compound Classification Based on Principal Component Analysis.
J. Chem. Inf. Comput. Sci., 1999

Database Searching for Compounds with Similar Biological Activity Using Short Binary Bit String Representations of Molecules.
J. Chem. Inf. Comput. Sci., 1999

Binary Quantitative Structure-Activity Relationship (QSAR) Analysis of Estrogen Receptor Ligands.
J. Chem. Inf. Comput. Sci., 1999

Statistical analysis of computational docking of large compound data bases to distinct protein binding sites.
J. Comput. Chem., 1999

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

Computer-Aided Drug Design - Session Introduction.
Proceedings of the 4th Pacific Symposium on Biocomputing, 1999

1997
Prediction of the three-dimensional structure of the human Fas receptor by comparative molecular modeling.
J. Comput. Aided Mol. Des., 1997


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