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LiGen: A High Performance Workflow for Chemistry Driven de Novo Design

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What this work says

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

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<490::aid-jcc1>3.0.co;2-popenalex-snapshot

Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<520::aid-jcc2>3.0.co;2-wopenalex-snapshot

Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<553::aid-jcc3>3.0.co;2-topenalex-snapshot

Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<587::aid-jcc4>3.0.co;2-qopenalex-snapshot

Merck molecular force field. IV. conformational energies and geometries for MMFF94

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<616::aid-jcc5>3.0.co;2-xopenalex-snapshot

Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules

inferredcites →https://doi.org/10.1002/9780470915110.ch11openalex-snapshot

Fragment‐Based Drug Design: Considerations for Good ADME Properties

inferredcites →https://doi.org/10.1002/prot.340190305openalex-snapshot

HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site

inferredcites →https://doi.org/10.1007/bf00117275openalex-snapshot

PRO_LIGAND: An approach to de novo molecular design. 1. Application to the design of organic molecules

inferredcites →https://doi.org/10.1007/bf00124387openalex-snapshot

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/s10822-006-9091-xopenalex-snapshot

Ultrafast de novo docking combining pharmacophores and combinatorics

inferredcites →https://doi.org/10.1007/s10822-009-9291-2openalex-snapshot

Second-generation de novo design: a view from a medicinal chemist perspective

inferredcites →https://doi.org/10.1016/j.bmcl.2009.01.034openalex-snapshot

Design and synthesis of new hydroxyethylamines as inhibitors of d-alanyl-d-lactate ligase (VanA) and d-alanyl-d-alanine ligase (DdlB)

inferredcites →https://doi.org/10.1016/j.ejmech.2009.11.054openalex-snapshot

Design, synthesis and evaluation of analogs of initiation factor 4E (eIF4E) cap-binding antagonist Bn7-GMP

inferredcites →https://doi.org/10.1021/ci00017a027openalex-snapshot

SPROUT: Recent developments in the de novo design of molecules

inferredcites →https://doi.org/10.1021/ci050324copenalex-snapshot

A Knowledge-Based Weighting Approach to Ligand-Based Virtual Screening

inferredcites →https://doi.org/10.1021/ci060094hopenalex-snapshot

Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations

inferredcites →https://doi.org/10.1021/ci100350uopenalex-snapshot

LigBuilder 2: A Practical de Novo Drug Design Approach

inferredcites →https://doi.org/10.1021/ci300415dopenalex-snapshot

Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17

inferredcites →https://doi.org/10.1021/ci700424bopenalex-snapshot

Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization

inferredcites →https://doi.org/10.1021/ci800308hopenalex-snapshot

De Novo Drug Design Using Multiobjective Evolutionary Graphs

inferredcites →https://doi.org/10.1021/jm00049a019openalex-snapshot

PRO_LIGAND: An Approach to de Novo Molecular Design. 2. Design of Novel Molecules from Molecular Field Analysis (MFA) Models and Pharmacophores

inferredcites →https://doi.org/10.1021/jm00064a003openalex-snapshot

GroupBuild: a fragment-based method for de novo drug design

inferredcites →https://doi.org/10.1021/jm0103256openalex-snapshot

Structure-Based Generation of a New Class of Potent Cdk4 Inhibitors: New de Novo Design Strategy and Library Design

inferredcites →https://doi.org/10.1021/jm030809xopenalex-snapshot

SYNOPSIS: SYNthesize and OPtimize System in Silico

inferredcites →https://doi.org/10.1023/a:1008124202956openalex-snapshot

Fast prediction and visualization of protein binding pockets with PASS

inferredcites →https://doi.org/10.1038/nrd1799openalex-snapshot

Computer-based de novo design of drug-like molecules

inferredcites →https://doi.org/10.1039/9781847558879-00217openalex-snapshot

Fragment-based De Novo Design of Drug-like Molecules

inferredcites →https://doi.org/10.1186/1758-2946-1-8openalex-snapshot

Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions

inferredcites →https://doi.org/10.1201/9781420082999-c10openalex-snapshot

Computer-Aided Molecular Design

inferredcites →https://doi.org/10.1371/journal.pcbi.1002380openalex-snapshot

DOGS: Reaction-Driven de novo Design of Bioactive Compounds

inferredcites →https://doi.org/10.1517/17460441.2010.497534openalex-snapshot

De novodesign: balancing novelty and confined chemical space

inferredcites →https://doi.org/10.2174/138955712802762284openalex-snapshot

Multi-Objective Optimization Methods in De Novo Drug Design

inferredcites →https://doi.org/10.2174/157340611796150905openalex-snapshot

Computer-Aided Design, Synthesis, and Biological Activity Evaluation of Potent Fusion Inhibitors Targeting HIV-1 gp41

What points at this work

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

inferred← citeshttps://doi.org/10.1002/jcc.25052openalex-snapshot

Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets

inferred← citeshttps://doi.org/10.1002/jmr.2471openalex-snapshot

Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

inferred← citeshttps://doi.org/10.1002/minf.201800059openalex-snapshot

Chemistry‐driven Hit‐to‐lead Optimization Guided by Structure‐based Approaches

inferred← citeshttps://doi.org/10.1002/wcms.1529openalex-snapshot

Rational design of allosteric modulators: Challenges and successes

inferred← citeshttps://doi.org/10.1007/978-1-0716-4003-6_7openalex-snapshot

Approaching Pharmacological Space: Events and Components

inferred← citeshttps://doi.org/10.1007/978-3-031-30691-4_2openalex-snapshot

A European Drug-Discovery Platform: From In Silico to Experimental Validation

inferred← citeshttps://doi.org/10.1007/978-3-031-30691-4_4openalex-snapshot

The High-Performance Computing Resources for the EXSCALATE4CoV Project

inferred← citeshttps://doi.org/10.1007/s11227-020-03295-xopenalex-snapshot

Tunable approximations to control time-to-solution in an HPC molecular docking Mini-App

inferred← citeshttps://doi.org/10.1016/b978-0-12-822312-3.00011-4openalex-snapshot

Modern Tools and Techniques in Computer-Aided Drug Design

inferred← citeshttps://doi.org/10.1016/j.biopha.2019.109764openalex-snapshot

Inhibition of osteoclast activity by complement regulation with DF3016A, a novel small-molecular-weight C5aR inhibitor

inferred← citeshttps://doi.org/10.1016/j.future.2024.03.045openalex-snapshot

Enabling performance portability on the LiGen drug discovery pipeline

inferred← citeshttps://doi.org/10.1016/j.future.2025.107863openalex-snapshot

Harnessing quality-throughput trade-off in scoring functions for extreme-scale virtual screening campaigns

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.139590openalex-snapshot

Cys44 of SARS-CoV-2 3CLpro affects its catalytic activity

inferred← citeshttps://doi.org/10.1016/j.jpdc.2023.104819openalex-snapshot

GPU-optimized approaches to molecular docking-based virtual screening in drug discovery: A comparative analysis

inferred← citeshttps://doi.org/10.1016/j.softx.2018.03.006openalex-snapshot

libVersioningCompiler: An easy-to-use library for dynamic generation and invocation of multiple code versions

inferred← citeshttps://doi.org/10.1016/j.trechm.2020.11.004openalex-snapshot

Defining and Exploring Chemical Spaces

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01745openalex-snapshot

MARS Plus: An Improved Molecular Design Tool for Complex Compounds Involving Ionic, Stereo, and Cis–Trans Isomeric Structures

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00691openalex-snapshot

AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization

inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02199openalex-snapshot

Condensation of Force Field Parameters from Machine Learning Predicted Distributions for High-Throughput Virtual Screening Applications

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00020openalex-snapshot

BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b01197openalex-snapshot

Cov_FB3D: A De Novo Covalent Drug Design Protocol Integrating the BA-SAMP Strategy and Machine-Learning-Based Synthetic Tractability Evaluation

inferred← citeshttps://doi.org/10.1021/acsptsci.0c00216openalex-snapshot

Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen

inferred← citeshttps://doi.org/10.1021/ci400079kopenalex-snapshot

Use of Experimental Design To Optimize Docking Performance: The Case of LiGenDock, the Docking Module of Ligen, a New De Novo Design Program

inferred← citeshttps://doi.org/10.1021/ci400418copenalex-snapshot

De Novo Design of Drug-Like Molecules by a Fragment-Based Molecular Evolutionary Approach

inferred← citeshttps://doi.org/10.1021/ci4007497openalex-snapshot

Automated Design of Realistic Organometallic Molecules from Fragments

inferred← citeshttps://doi.org/10.1021/ci5006355openalex-snapshot

Evaluation of a Semi-Automated Workflow for Fragment Growing

inferred← citeshttps://doi.org/10.1038/s41597-022-01532-xopenalex-snapshot

Cytopathic SARS-CoV-2 screening on VERO-E6 cells in a large-scale repurposing effort

inferred← citeshttps://doi.org/10.1038/s41598-017-11194-0openalex-snapshot

Novel selective, potent naphthyl TRPM8 antagonists identified through a combined ligand- and structure-based virtual screening approach

inferred← citeshttps://doi.org/10.1088/2058-9565/ae0890openalex-snapshot

Molecular docking via weighted subgraph isomorphism on quantum annealers

inferred← citeshttps://doi.org/10.1089/cmb.2016.0056openalex-snapshot

Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach

inferred← citeshttps://doi.org/10.1109/cse.2015.58openalex-snapshot

ANTAREX -- AutoTuning and Adaptivity appRoach for Energy Efficient eXascale HPC Systems

inferred← citeshttps://doi.org/10.1109/pdsw54622.2021.00007openalex-snapshot

Understanding the I/O Impact on the Performance of High-Throughput Molecular Docking

inferred← citeshttps://doi.org/10.1109/qce60285.2024.00066openalex-snapshot

An Experimental Approach to Quantum Molecular Docking

inferred← citeshttps://doi.org/10.1145/2903150.2903470openalex-snapshot

The ANTAREX approach to autotuning and adaptivity for energy efficient HPC systems

inferred← citeshttps://doi.org/10.1145/3203217.3205338openalex-snapshot

Autotuning and adaptivity in energy efficient HPC systems

inferred← citeshttps://doi.org/10.1145/3235830.3235835openalex-snapshot

Accelerating a Geometric Approach to Molecular Docking with OpenACC

inferred← citeshttps://doi.org/10.1145/3528416.3530872openalex-snapshot

An extreme-scale virtual screening platform for drug discovery

inferred← citeshttps://doi.org/10.1145/3529538.3529688openalex-snapshot

Towards a Portable Drug Discovery Pipeline with SYCL 2020

inferred← citeshttps://doi.org/10.1145/3587135.3592172openalex-snapshot

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale

inferred← citeshttps://doi.org/10.1145/3636480.3637095openalex-snapshot

High-throughput drug discovery on the Fujitsu A64FX architecture

inferred← citeshttps://doi.org/10.1186/s13321-020-00431-wopenalex-snapshot

CReM: chemically reasonable mutations framework for structure generation

inferred← citeshttps://doi.org/10.2174/1568026614666140929115506openalex-snapshot

Revisiting De Novo Drug Design: Receptor Based Pharmacophore Screening

inferred← citeshttps://doi.org/10.2751/jcac.16.15openalex-snapshot

A Mini-review on Chemoinformatics Approaches for Drug Discovery

inferred← citeshttps://doi.org/10.3389/fphar.2023.1148670openalex-snapshot

Ensemble of structure and ligand-based classification models for hERG liability profiling

inferred← citeshttps://doi.org/10.3390/ijms21072265openalex-snapshot

Combining Molecular Dynamics and Docking Simulations to Develop Targeted Protocols for Performing Optimized Virtual Screening Campaigns on the hTRPM8 Channel

inferred← citeshttps://doi.org/10.3390/ijms21207677openalex-snapshot

Binding Mode Exploration of B1 Receptor Antagonists’ by the Use of Molecular Dynamics and Docking Simulation—How Different Target Engagement Can Determine Different Biological Effects

inferred← citeshttps://doi.org/10.3390/ijms23147558openalex-snapshot

Extensive Sampling of Molecular Dynamics Simulations to Identify Reliable Protein Structures for Optimized Virtual Screening Studies: The Case of the hTRPM8 Channel

inferred← citeshttps://doi.org/10.3390/ijms25010450openalex-snapshot

Target Prediction by Multiple Virtual Screenings: Analyzing the SARS-CoV-2 Phenotypic Screening by the Docking Simulations Submitted to the MEDIATE Initiative

inferred← citeshttps://doi.org/10.3390/molecules26040797openalex-snapshot

Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease

inferred← citeshttps://doi.org/10.3390/ph15010063openalex-snapshot

A Review on Parallel Virtual Screening Softwares for High-Performance Computers

inferred← citeshttps://doi.org/10.3850/9783981537079_1012openalex-snapshot

AutoTuning and Adaptivity appRoach for Energy Efficient eXascale HPC Systems: The ANTAREX Approach

inferred← citeshttps://doi.org/10.6084/m9.figshare.12178002openalex-snapshot

Additional file 1 of CReM: chemically reasonable mutations framework for structure generation

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