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GARLig: A Fully Automated Tool for Subset Selection of Large Fragment Spaces via a Self-Adaptive Genetic Algorithm

https://doi.org/10.1021/ci9003305
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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KNOBLE: A Knowledge‐Based Approach for the Design and Synthesis of Readily Accessible Small‐Molecule Chemical Probes To Test Protein Binding
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FlexNovo : Structure‐Based Searching in Large Fragment Spaces
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From Molecular Shape to Potent Bioactive Agents II: Fragment‐Based de novo Design
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The refined 1.9 A crystal structure of human alpha‐thrombin: interaction with D‐Phe‐Pro‐Arg chloromethylketone and significance of the Tyr‐Pro‐Pro‐Trp insertion segment.
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Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin.
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A semiempirical free energy force field with charge‐based desolvation
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Improved protein–ligand docking using GOLD
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Experimental Research in Evolutionary Computation: The New Experimentalism
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CAVEAT: A program to facilitate the design of organic molecules
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The computer program LUDI: A new method for the de novo design of enzyme inhibitors
inferredcites →https://doi.org/10.1007/bf00124404openalex-snapshot
PRO_LIGAND: An approach to de novo molecular design. 3. A genetic algorithm for structure refinement
inferredcites →https://doi.org/10.1007/s10822-005-9015-1openalex-snapshot
ENPDA: an evolutionary structure-based de novo peptide design algorithm
inferredcites →https://doi.org/10.1016/j.jmb.2006.04.024openalex-snapshot
From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase
inferredcites →https://doi.org/10.1016/s0169-409x(00)00129-0openalex-snapshot
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1
inferredcites →https://doi.org/10.1016/s1074-5521(97)90073-9openalex-snapshot
Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D
inferredcites →https://doi.org/10.1016/s1093-3263(00)00060-7openalex-snapshot
Designing targeted libraries with genetic algorithms
inferredcites →https://doi.org/10.1021/bi00177a018openalex-snapshot
Crystallographic Structures of Thrombin Complexed with Thrombin Receptor Peptides: Existence of Expected and Novel Binding Modes
inferredcites →https://doi.org/10.1021/bi9622231openalex-snapshot
Molecular Design and Characterization of an α-Thrombin Inhibitor Containing a Novel P1 Moiety
inferredcites →https://doi.org/10.1021/ci000038vopenalex-snapshot
Ultrafast Algorithm for Designing Focused Combinational Arrays
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Combinatorial Library Design Using a Multiobjective Genetic Algorithm
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A Fast Exchange Algorithm for Designing Focused Libraries in Lead Optimization
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Flux (1): A Virtual Synthesis Scheme for Fragment-Based de Novo Design
inferredcites →https://doi.org/10.1021/ci700424bopenalex-snapshot
Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization
inferredcites →https://doi.org/10.1021/ci8001205openalex-snapshot
Identification of Hits and Lead Structure Candidates with Limited Resources by Adaptive Optimization
inferredcites →https://doi.org/10.1021/ci980103popenalex-snapshot
Rational Combinatorial Library Design. 3. Simulated Annealing Guided Evaluation (SAGE) of Molecular Diversity: A Novel Computational Tool for Universal Library Design and Database Mining
inferredcites →https://doi.org/10.1021/ja953172iopenalex-snapshot
Application of Genetic Algorithms to Combinatorial Synthesis: A Computational Approach to Lead Identification and Lead Optimization,
inferredcites →https://doi.org/10.1021/jm010833fopenalex-snapshot
Statistical Molecular Design, Parallel Synthesis, and Biological Evaluation of a Library of Thrombin Inhibitors
inferredcites →https://doi.org/10.1021/jm030809xopenalex-snapshot
SYNOPSIS: SYNthesize and OPtimize System in Silico
inferredcites →https://doi.org/10.1021/jm050436vopenalex-snapshot
DrugScore CSD Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction
inferredcites →https://doi.org/10.1021/jm070750kopenalex-snapshot
Tagged Fragment Method for Evolutionary Structure-Based De Novo Lead Generation and Optimization
inferredcites →https://doi.org/10.1021/jm970033yopenalex-snapshot
Designing Combinatorial Library Mixtures Using a Genetic Algorithm
inferredcites →https://doi.org/10.1021/jm970403iopenalex-snapshot
New Methodology for Profiling Combinatorial Libraries and Screening Sets: Cleaning Up the Design Process with HARPick
inferredcites →https://doi.org/10.1021/jm9704107openalex-snapshot
Dibasic Benzo[b]thiophene Derivatives as a Novel Class of Active Site-Directed Thrombin Inhibitors. 1. Determination of the Serine Protease Selectivity, Structure−Activity Relationships, and Binding Orientation
inferredcites →https://doi.org/10.1023/a:1008036704754openalex-snapshot
CombiDOCK: Structure-based combinatorial docking and library design
inferredcites →https://doi.org/10.1023/a:1008040531766openalex-snapshot
Combinatorial docking and combinatorial chemistry: Design of potent non-peptide thrombin inhibitors
inferredcites →https://doi.org/10.1023/a:1008108423895openalex-snapshot
A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm
inferredcites →https://doi.org/10.1023/a:1008184403558openalex-snapshot
De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks
inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
inferredcites →https://doi.org/10.1023/a:1014389729000openalex-snapshot
A genetic algorithm for structure-based de novo design
inferredcites →https://doi.org/10.1038/nrd1799openalex-snapshot
Computer-based de novo design of drug-like molecules
inferredcites →https://doi.org/10.1073/pnas.0501983102openalex-snapshot
Thrombin inhibitors identified by computer-assisted multiparameter design
inferredcites →https://doi.org/10.1073/pnas.140132697openalex-snapshot
Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries
inferredcites →https://doi.org/10.1093/oso/9780195099713.001.0001openalex-snapshot
Evolutionary Algorithms in Theory and Practice
inferredcites →https://doi.org/10.1162/106365601750190406openalex-snapshot
Self-Adaptive Genetic Algorithms with Simulated Binary Crossover
inferredcites →https://doi.org/10.2174/1386207024607400openalex-snapshot
Rational Principles of Compound Selection for Combinatorial Library Design
inferredcites →https://doi.org/10.5860/choice.27-0936openalex-snapshot
Genetic algorithms in search, optimization, and machine learning

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/9783527677016.ch1openalex-snapshot
De NovoDesign: From Models to Molecules
inferred← citeshttps://doi.org/10.1002/9783527677016.ch15openalex-snapshot
Fragment‐Based Design of Focused Compound Libraries
inferred← citeshttps://doi.org/10.1002/wcms.49openalex-snapshot
Enabling future drug discovery by de novo design
inferred← citeshttps://doi.org/10.1007/978-3-319-06508-3_11openalex-snapshot
In silico Maturation: Processing Sequences to Improve Biopolymer Functions Based on Genetic Algorithms
inferred← citeshttps://doi.org/10.1007/978-981-99-9704-6_6openalex-snapshot
CavFind: A Novel Algorithm to Detect Cavities on Protein Structure
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01964openalex-snapshot
Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space
inferred← citeshttps://doi.org/10.1021/ct300190uopenalex-snapshot
Optimization of a Genetic Algorithm for the Functionalization of Fullerenes
inferred← citeshttps://doi.org/10.1039/d6ra05468dopenalex-snapshot
Molecular recognition of a Novel thiazolidinedione–morpholine-based ionic liquid salt by HSA: spectroscopic and molecular dynamics analysis
inferred← citeshttps://doi.org/10.1063/1.3656323openalex-snapshot
Optimization of a genetic algorithm for searching molecular conformer space
inferred← citeshttps://doi.org/10.1111/cgf.13158openalex-snapshot
Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey
inferred← citeshttps://doi.org/10.1517/17460441.2011.554394openalex-snapshot
The quest for novel chemical matter and the contribution of computer-aidedde novodesign
inferred← citeshttps://doi.org/10.2174/138955712802762284openalex-snapshot
Multi-Objective Optimization Methods in De Novo Drug Design
inferred← citeshttps://doi.org/10.2174/1568026614666140929115506openalex-snapshot
Revisiting De Novo Drug Design: Receptor Based Pharmacophore Screening
inferred← citeshttps://doi.org/10.3233/jcm-190026openalex-snapshot
Multi niche crowding genetic algorithm parameter tuning for molecular potential energy surface computation
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