| Q47501489 | 10th ICCS/GCC Conference: 40 Years of Cheminformatics |
| Q103810756 | A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses |
| Q28282247 | A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function |
| Q52298930 | A fast flexible docking method using an incremental construction algorithm. |
| Q45789560 | A flexible-hydrogen interaction model for protein-ligand docking. |
| Q40811884 | ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations |
| Q46403940 | Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web. |
| Q45789112 | Aligning chemical structure diagrams with local search. |
| Q35201046 | An integrated approach to knowledge-driven structure-based virtual screening |
| Q43852582 | Analyzing the topology of active sites: on the prediction of pockets and subpockets |
| Q51997292 | Automated drawing of structural molecular formulas under constraints. |
| Q30840167 | Benchmark data sets for structure-based computational target prediction |
| Q47664899 | Benchmarking Commercial Conformer Ensemble Generators |
| Q33428199 | Beyond the virtual screening paradigm: structure-based searching for new lead compounds |
| Q52281039 | CASP2 experiences with docking flexible ligands using FlexX. |
| Q34912659 | CONFECT: conformations from an expert collection of torsion patterns |
| Q55009516 | Chemical pattern visualization in 2D – the SMARTSviewer. |
| Q42627755 | Combining global and local measures for structure-based druggability predictions |
| Q92268983 | Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis |
| Q92239732 | Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms |
| Q47133011 | Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation. |
| Q57009127 | Computational biotechnology: Prediction of competitive substrate inhibition of enzymes by buffer compounds with protein–ligand docking |
| Q34396832 | Computational methods for biomolecular docking. |
| Q45965923 | Conformational sampling for large-scale virtual screening: accuracy versus ensemble size. |
| Q62669365 | Conformator: A Novel Method for the Generation of Conformer Ensembles |
| Q90941920 | Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration |
| Q39391755 | Consistent two-dimensional visualization of protein-ligand complex series |
| Q51531786 | De novo design by pharmacophore-based searches in fragment spaces. |
| Q34093449 | Design of combinatorial libraries for the exploration of virtual hits from fragment space searches with LoFT. |
| Q30985789 | Detailed analysis of scoring functions for virtual screening |
| Q104482778 | Disconnected Maximum Common Substructures under Constraints |
| Q50867992 | Discriminative Chemical Patterns: Automatic and Interactive Design. |
| Q47987315 | DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment |
| Q51646570 | Docking of hydrophobic ligands with interaction-based matching algorithms. |
| Q39155730 | Drawing the PDB: Protein-Ligand Complexes in Two Dimensions |
| Q104619316 | Editorial: Method and Data Sharing and Reproducibility of Scientific Results |
| Q46341476 | Elucidating protein-protein interactions using the HYDE scoring function. |
| Q47859354 | Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures |
| Q39380134 | Evaluation of deoxyhypusine synthase inhibitors targeting BCR-ABL positive leukemias |
| Q35572263 | Evidence of water molecules--a statistical evaluation of water molecules based on electron density |
| Q38191683 | Exploiting structural information for drug-target assessment |
| Q113588018 | Exploration of Ultralarge Compound Collections for Drug Discovery |
| Q51911690 | Exploring fragment spaces under multiple physicochemical constraints. |
| Q47358315 | Exploring structure-activity relationships with three-dimensional matched molecular pairs - A review. |
| Q36129841 | FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption |
| Q38666538 | Facing the challenges of computational target prediction |
| Q44024866 | Facing the challenges of structure-based target prediction by inverse virtual screening |
| Q27998699 | Fast automated placement of polar hydrogen atoms in protein-ligand complexes |
| Q50561057 | Fast force field-based optimization of protein-ligand complexes with graphics processor. |
| Q34580305 | Fast protein binding site comparison via an index-based screening technology |
| Q40134572 | Feasibility of Active Machine Learning for Multiclass Compound Classification |
| Q51647018 | Feature trees: a new molecular similarity measure based on tree matching. |
| Q51610424 | Flat and Easy: 2D Depiction of Protein-Ligand Complexes. |
| Q30328164 | FlexE: efficient molecular docking considering protein structure variations. |
| Q51935607 | FlexNovo: structure-based searching in large fragment spaces. |
| Q45070169 | FlexX-Scan: fast, structure-based virtual screening |
| Q44109232 | Flexible docking under pharmacophore type constraints |
| Q61940500 | Force-field-based minimizations of protein-ligand complexes in the blink of an eye |
| Q57009154 | From Structure Diagrams to Visual Chemical Patterns |
| Q44268445 | From activity cliffs to target-specific scoring models and pharmacophore hypotheses |
| Q51917215 | From modeling to medicinal chemistry: automatic generation of two-dimensional complex diagrams. |
| Q51945190 | Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies. |
| Q98180662 | GeoMine: Interactive Pattern Mining of Protein-Ligand Interfaces in the Protein Data Bank |
| Q57009144 | HYDEing the false positives – scoring for lead optimization |
| Q38958067 | High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators |
| Q46502091 | Hydrogen placement in protein-ligand complexes under consideration of tautomerism. |
| Q51610986 | Identification of Inhibitors of the Tyrosine Kinase c-Met by Structure-Based Virtual Screening. |
| Q33994901 | Improving similarity-driven library design: customized matching and regioselective feature trees |
| Q62669359 | In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening |
| Q30391029 | In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding |
| Q42232416 | In silico design, synthesis, and screening of novel deoxyhypusine synthase inhibitors targeting HIV-1 replication |
| Q30397969 | Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces |
| Q38080968 | Interactive design of generic chemical patterns |
| Q32177442 | Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein-Ligand Interfaces |
| Q55669139 | Let's talk about rings. |
| Q57009110 | Letter from the Editors |
| Q38806965 | Linker-Region Modified Derivatives of the Deoxyhypusine Synthase Inhibitor CNI-1493 Suppress HIV-1 Replication |
| Q33519628 | LoFT: similarity-driven multiobjective focused library design |
| Q41767543 | MONA - Interactive manipulation of molecule collections |
| Q35781761 | MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing |
| Q57009076 | Machine Learning in Drug Discovery |
| Q62669363 | Machine Learning in Drug Discovery |
| Q115926452 | Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces |
| Q30366129 | Modeling of metal interaction geometries for protein-ligand docking. |
| Q48449911 | Molecular complexes at a glance: automated generation of two-dimensional complex diagrams. |
| Q52260133 | Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention. |
| Q45286908 | Multiple-ligand-based virtual screening: methods and applications of the MTree approach |
| Q48565552 | NAOMI: on the almost trivial task of reading molecules from different file formats. |
| Q47692054 | NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures |
| Q36091294 | Nearly no Scoring Function Without a Hansch-Analysis |
| Q40533405 | Novel technologies for virtual screening |
| Q51869169 | On the art of compiling and using 'drug-like' chemical fragment spaces. |
| Q57009083 | Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples |
| Q52311354 | Placement of medium-sized molecular fragments into active sites of proteins. |
| Q50300604 | PoseView -- molecular interaction patterns at a glance. |
| Q43872323 | Predicting enzymatic function from global binding site descriptors |
| Q50296051 | Prediction of kinase inhibitors cross-reaction on the basis of kinase ATP cavity similarities: a study using PKSIM protein similarity score. |
| Q30401819 | Prediction of protein mutation effects based on dehydration and hydrogen bonding - A large-scale study |
| Q50872388 | Protein pocket and ligand shape comparison and its application in virtual screening. |
| Q113436954 | ProteinsPlus: a comprehensive collection of web-based molecular modeling tools |
| Q91984443 | ProteinsPlus: interactive analysis of protein-ligand binding interfaces |
| Q39556598 | Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes |
| Q46970226 | Reading PDB: perception of molecules from 3D atomic coordinates |
| Q45166891 | Recore: a fast and versatile method for scaffold hopping based on small molecule crystal structure conformations |
| Q36267216 | RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases |
| Q30383471 | SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. |
| Q27144426 | Scientific competency questions as the basis for semantically enriched open pharmacological space development |
| Q39404870 | Searching for recursively defined generic chemical patterns in nonenumerated fragment spaces |
| Q48042862 | Searching for substructures in fragment spaces |
| Q57009149 | Searching substructures in fragment spaces |
| Q33475687 | Second-generation de novo design: a view from a medicinal chemist perspective |
| Q102070219 | Shape-Based Descriptors for Efficient Structure-Based Fragment Growing |
| Q43701172 | Similarity searching in large combinatorial chemistry spaces |
| Q57009135 | Some thoughts on the “A” in computer-aided molecular design |
| Q39671594 | Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function |
| Q51626371 | SwiFT: an index structure for reduced graph descriptors in virtual screening and clustering. |
| Q41893290 | Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2 |
| Q45789343 | Systematic search for pairwise dependencies of torsion angles. |
| Q44319486 | TFD: Torsion Fingerprints as a new measure to compare small molecule conformations |
| Q30395448 | The Art of Compiling Protein Binding Site Ensembles |
| Q47252936 | The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. |
| Q42090472 | The Internet as Scientific Knowledge Base: Navigating the Chem-Bio Space |
| Q52214244 | The particle concept: placing discrete water molecules during protein-ligand docking predictions. |
| Q46534004 | The valence state combination model: a generic framework for handling tautomers and protonation states |
| Q52361618 | Time-efficient docking of flexible ligands into active sites of proteins. |
| Q100754705 | Topological Similarity Search in Large Combinatorial Fragment Spaces |
| Q35872047 | Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules. |
| Q34573730 | Torsion angle preferences in druglike chemical space: a comprehensive guide |
| Q61940501 | TorsionAnalyzer: exploring conformational space |
| Q57009165 | Towards an Integrated Description of Hydrogen Bonding and Dehydration: Decreasing False Positives in Virtual Screening with the HYDE Scoring Function |
| Q33273270 | TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time |
| Q33179085 | Two-stage method for protein-ligand docking |
| Q36030008 | UNICON: A Powerful and Easy-to-Use Compound Library Converter |
| Q48048183 | Unique ring families: a chemically meaningful description of molecular ring topologies |
| Q48658624 | What is the potential of structure-based target prediction methods? |
| Q46879350 | Where are the boundaries? Automated pocket detection for druggability studies. |
| Q39449589 | mRAISE: an alternative algorithmic approach to ligand-based virtual screening |