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Retrospective Docking Study of PDE4B Ligands and an Analysis of the Behavior of Selected Scoring Functions
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Critical evaluation of search algorithms for automated molecular docking and database screening
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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High throughput docking for library design and library prioritization
inferredcites →https://doi.org/10.1002/prot.10115openalex-snapshot
Principles of docking: An overview of search algorithms and a guide to scoring functions
inferredcites →https://doi.org/10.1002/prot.10465openalex-snapshot
Improved protein–ligand docking using GOLD
inferredcites →https://doi.org/10.1002/prot.340080302openalex-snapshot
Automated docking of substrates to proteins by simulated annealing
inferredcites →https://doi.org/10.1006/jmbi.1996.0477openalex-snapshot
A Fast Flexible Docking Method using an Incremental Construction Algorithm
inferredcites →https://doi.org/10.1006/jmbi.1996.0897openalex-snapshot
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot
Knowledge-based scoring function to predict protein-ligand interactions
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The computer program LUDI: A new method for the de novo design of enzyme inhibitors
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Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
inferredcites →https://doi.org/10.1016/0022-2836(82)90153-xopenalex-snapshot
A geometric approach to macromolecule-ligand interactions
inferredcites →https://doi.org/10.1016/1074-5521(95)90050-0openalex-snapshot
Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
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Computational approaches to structure-based ligand design
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Design, synthesis and structure–activity relationships of a series of 9-substituted adenine derivatives as selective phosphodiesterase type-4 inhibitors
inferredcites →https://doi.org/10.1016/s1074-5521(96)90093-9openalex-snapshot
Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites
inferredcites →https://doi.org/10.1016/s1093-3263(02)00164-xopenalex-snapshot
LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
inferredcites →https://doi.org/10.1021/ci00008a019openalex-snapshot
A combined model-building and distance-geometry approach to automated conformational analysis and search
inferredcites →https://doi.org/10.1021/ci034289qopenalex-snapshot
Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment
inferredcites →https://doi.org/10.1021/jm00026a001openalex-snapshot
Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes
inferredcites →https://doi.org/10.1021/jm0003992openalex-snapshot
Detailed Analysis of Scoring Functions for Virtual Screening
inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
inferredcites →https://doi.org/10.1021/jm0100279openalex-snapshot
Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System
inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm990073xopenalex-snapshot
Evaluation of PMF Scoring in Docking Weak Ligands to the FK506 Binding Protein
inferredcites →https://doi.org/10.1021/jm990352kopenalex-snapshot
Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
inferredcites →https://doi.org/10.1023/a:1007907728892openalex-snapshot
QXP: Powerful, rapid computer algorithms for structure-based drug design
inferredcites →https://doi.org/10.1023/a:1008005918983openalex-snapshot
MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
inferredcites →https://doi.org/10.1023/a:1008044721715openalex-snapshot
Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations
inferredcites →https://doi.org/10.1023/a:1008068903544openalex-snapshot
Scoring functions: A view from the bench
inferredcites →https://doi.org/10.1023/a:1008158231558openalex-snapshot
Deciphering common failures in molecular docking of ligand-protein complexes
inferredcites →https://doi.org/10.1126/science.257.5073.1078openalex-snapshot
Structure-Based Strategies for Drug Design and Discovery
inferredcites →https://doi.org/10.1515/bc.2001.168openalex-snapshot
Fragment-Based Flexible Ligand Docking by Evolutionary Optimization
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/0471266949.bmc140openalex-snapshot
Docking and Scoring in Drug Discovery
inferred← citeshttps://doi.org/10.1002/biot.200700259openalex-snapshot
Computational chemistry approaches to drug discovery in signal transduction
inferred← citeshttps://doi.org/10.1002/chir.20522openalex-snapshot
Investigation of the stereoselectivity of an anti‐amino acid antibody using molecular modeling and ligand docking
inferred← citeshttps://doi.org/10.1002/prot.21405openalex-snapshot
Structure‐based virtual ligand screening with LigandFit: Pose prediction and enrichment of compound collections
inferred← citeshttps://doi.org/10.1007/s10822-010-9356-2openalex-snapshot
Chemical space sampling by different scoring functions and crystal structures
inferred← citeshttps://doi.org/10.1007/s10822-022-00456-3openalex-snapshot
Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA
inferred← citeshttps://doi.org/10.1016/j.drudis.2006.03.009openalex-snapshot
Consensus scoring for protein–ligand interactions
inferred← citeshttps://doi.org/10.1016/j.febslet.2007.06.067openalex-snapshot
An apoptosis‐related gene network induced by novel compound‐cRGD in human breast cancer cells
inferred← citeshttps://doi.org/10.1016/j.jbiotec.2009.12.003openalex-snapshot
Integration of virtual screening with high-throughput screening for the identification of novel Rho-kinase I inhibitors
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.01.009openalex-snapshot
Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets
inferred← citeshttps://doi.org/10.1016/s1574-1400(06)02009-3openalex-snapshot
Chapter 9 Molecular Similarity: Advances in Methods, Applications and Validations in Virtual Screening and QSAR
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00068openalex-snapshot
Effective Reaction-Based De Novo Strategy for Kinase Targets: A Case Study on MERTK Inhibitors
inferred← citeshttps://doi.org/10.1021/ci050420dopenalex-snapshot
Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions
inferred← citeshttps://doi.org/10.1021/np300749wopenalex-snapshot
Benzoquinones and Terphenyl Compounds As Phosphodiesterase-4B Inhibitors from a Fungus of the Order Chaetothyriales (MSX 47445)
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Targeting Therapy for Breast Carcinoma by ATP Synthase Inhibitor Aurovertin B
inferred← citeshttps://doi.org/10.17192/z2007.0753openalex-snapshot
Leitstrukturoptimierung für Antiprotozoika und Erfolgreiche Leitstruktursuche für Metalloproteinasen: Ein Fragment-basiertes Virtuelles Screening Verfahren
inferred← citeshttps://doi.org/10.21203/rs.3.rs-957884/v1openalex-snapshot
Comprehensive Modeling and Molecular Docking of Phosphodiesterase Inhibitors
inferred← citeshttps://doi.org/10.71193/jmct.20250009openalex-snapshot
Phosphodiesterase-4 Inhibitors in COPD Therapy: A Review of Mechanisms, Limitations, and Emerging Opportunities
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