ArticleJournal of chemical information and modeling2020
Molassembler: Molecular Graph Construction, Modification, and Conformer Generation for Inorganic and Organic Molecules.
Article in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Rapid Generation of Transition-State Conformer Ensembles via Constrained Distance Geometry.Journal of chemical information and modeling · 2026Article
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- Graph neural networks for predicting metal-ligand coordination of transition metal complexes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Lifelong Machine Learning Potentials for Chemical Reaction Network Explorations.Journal of chemical theory and computation · 2025Article
- Automated Microsolvation for Minimum Energy Path Construction in Solution.Journal of chemical theory and computation · 2025Article
- Data-Driven Virtual Screening of Conformational Ensembles of Transition-Metal Complexes.Journal of chemical theory and computation · 2025Article
- Enantiospecific Synthesis of Planar Chiral Rhodium and Iridium Cyclopentadienyl Complexes: Enabling Streamlined and Computer-Guided Access to Highly Selective Catalysts for Asymmetric C-H Functionalizations.Journal of the American Chemical Society · 2024Article
- Heron: Visualizing and Controlling Chemical Reaction Explorations and Networks.The journal of physical chemistry. A · 2024Article
- Emerging Conformational-Analysis Protocols from the RTCONF55-16K Reaction Thermochemistry Conformational Benchmark Set.Journal of chemical theory and computation · 2024Article
- Partial to Total Generation of 3D Transition-Metal Complexes.Journal of chemical theory and computation · 2024Article
- Overcoming the Pitfalls of Computing Reaction Selectivity from Ensembles of Transition States.The journal of physical chemistry letters · 2024Article
- Nanoscale chemical reaction exploration with a quantum magnifying glass.Nature communications · 2024Article
- Uncertainty-Aware First-Principles Exploration of Chemical Reaction Networks.The journal of physical chemistry. A · 2024Article
- A human-machine interface for automatic exploration of chemical reaction networks.Nature communications · 2024Article
- MACE: Automated Assessment of Stereochemistry of Transition Metal Complexes and Its Applications in Computational Catalysis.Journal of chemical theory and computation · 2024Article
- Automated de Novo Design of Olefin Metathesis Catalysts: Computational and Experimental Analysis of a Simple Thermodynamic Design Criterion.Journal of chemical information and modeling · 2024Article
- Quantum chemical data generation as fill-in for reliability enhancement of machine-learning reaction and retrosynthesis planning.Digital discovery · 2023Article
- Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application.Journal of chemical information and modeling · 2023Article
- Architector for high-throughput cross-periodic table 3D complex building.Nature communications · 2023Article
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Authors and funding
2 authors.
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Abstract
We present the graph-based molecule software Molassembler for building organic and inorganic molecules. Molassembler provides algorithms for the construction of molecules built from any set of elements from the periodic table. In particular, polynuclear transition-metal complexes and clusters can be considered. Structural information is encoded as a graph. Stereocenter configurations are interpretable from Cartesian coordinates into an abstract index of permutation for an extensible set of polyhedral shapes. Substituents are distinguished through a ranking algorithm. Graph and stereocenter representations are freely modifiable, and the chiral state is propagated where possible through incurred ranking changes. Conformers are generated with full stereoisomer control by four spatial dimension Distance Geometry with a refinement error function including dihedral terms. Molecules are comparable by an extended graph isomorphism, and their representation is canonicalizeable. Molassembler is written in C++ and provides Python bindings.
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