ArticleJournal of computer-aided molecular design2017
ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs.
Article in Journal of computer-aided molecular design, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- 3DOpt: Benchmark for Automated Design of 3D Molecular Structures across the Periodic Table.Journal of chemical information and modeling · 2026Article
- Rapid Generation of Transition-State Conformer Ensembles via Constrained Distance Geometry.Journal of chemical information and modeling · 2026Article
- Blocking ASIP to Protect MC1R Signaling and Mitigate Melanoma Risk: An In Silico Study.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Multiscale Computational and Pharmacophore-Based Screening of ALK Inhibitors with Experimental Validation.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands.Journal of computer-aided molecular design · 2024Article
- From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product.Journal of computer-aided molecular design · 2024Article
- Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design.Journal of computer-aided molecular design · 2023Article
- High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment.Journal of chemical information and modeling · 2023Article
- Unmasking the True Identity of Rapamycin's Minor Conformer.Journal of natural products · 2023Article
- Ensemble determination by NMR data deconvolution.Nature reviews. Chemistry · 2023Review
- Cell-permeable chameleonic peptides: Exploiting conformational dynamics in de novo cyclic peptide design.Current opinion in structural biology · 2023Review
- A Distributional Model of Bound Ligand Conformational Strain: From Small Molecules up to Large Peptidic Macrocycles.Journal of medicinal chemistry · 2023Article
- A Guide to In Silico Drug Design.Pharmaceutics · 2022Review
- In silico virtual screening of lead compounds for major antigenic sites in respiratory syncytial virus fusion protein.Emergent materials · 2022Article
- Discovery and Biosynthesis of a Structurally Dynamic Antibacterial Diterpenoid.Angewandte Chemie (International ed. in English) · 2021Article
- Geometrically Diverse Lariat Peptide Scaffolds Reveal an Untapped Chemical Space of High Membrane Permeability.Journal of the American Chemical Society · 2021Article
- Benchmark of Generic Shapes for Macrocycles.Journal of chemical information and modeling · 2020Article
- Conformational analysis of macrocycles: comparing general and specialized methods.Journal of computer-aided molecular design · 2020Article
- Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- Prediction of Passive Membrane Permeability by Semi-Empirical Method Considering Viscous and Inertial Resistances and Different Rates of Conformational Change and Diffusion.Molecular informatics · 2020Article
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2 authors.
Funding
Abstract
We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules. ForceGen is novel, avoiding use of distance geometry, molecular templates, or simulation-oriented stochastic sampling. The method is primarily driven by the molecular force field, implemented using an extension of MMFF94s and a partial charge estimator based on electronegativity-equalization. The force field is coupled to algorithms for direct sampling of realistic physical movements made by small molecules. Results are presented on a standard benchmark from the Cambridge Crystallographic Database of 480 drug-like small molecules, including full structure generation from SMILES strings. Reproduction of protein-bound crystallographic ligand poses is demonstrated on four carefully curated data sets: the ConfGen Set (667 ligands), the PINC cross-docking benchmark (1062 ligands), a large set of macrocyclic ligands (182 total with typical ring sizes of 12-23 atoms), and a commonly used benchmark for evaluating macrocycle conformer generation (30 ligands total). Results compare favorably to alternative methods, and performance on macrocyclic compounds approaches that observed on non-macrocycles while yielding a roughly 100-fold speed improvement over alternative MD-based methods with comparable performance.
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