ArticleJournal of cheminformatics2014
Molpher: a software framework for systematic chemical space exploration.
Article in Journal of cheminformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Scaffold-based evaluation metrics for fair comparison of molecular generators.Journal of cheminformatics · 2026Article
- A molecule perturbation software library and its application to study the effects of molecular design constraints.Journal of cheminformatics · 2023Article
- Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives.Life (Basel, Switzerland) · 2021Review
- GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics.Journal of cheminformatics · 2021Article
- Beyond generative models: superfast traversal, optimization, novelty, exploration and discovery (STONED) algorithm for molecules using SELFIES.Chemical science · 2021Article
- Profiling and analysis of chemical compounds using pointwise mutual information.Journal of cheminformatics · 2021Article
- SYBA: Bayesian estimation of synthetic accessibility of organic compounds.Journal of cheminformatics · 2020Article
- CReM: chemically reasonable mutations framework for structure generation.Journal of cheminformatics · 2020Article
- Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0.Journal of cheminformatics · 2017Article
- Consensus queries in ligand-based virtual screening experiments.Journal of cheminformatics · 2017Article
- The octet rule in chemical space: generating virtual molecules.Molecular diversity · 2017Article
- Nonpher: computational method for design of hard-to-synthesize structures.Journal of cheminformatics · 2017Article
- Open source molecular modeling.Journal of molecular graphics & modelling · 2016Review
- Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization.Journal of cheminformatics · 2016Article
- Web-based 3D-visualization of the DrugBank chemical space.Journal of cheminformatics · 2016Article
- Prediction-driven matched molecular pairs to interpret QSARs and aid the molecular optimization process.Journal of cheminformatics · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the discovery of either novel drugs or new tools for chemical biology.
resultsIn this paper, we describe Molpher, an open-source framework for the systematic exploration of chemical space. Through a process we term 'molecular morphing', Molpher produces a path of structurally-related compounds. This path is generated by the iterative application of so-called 'morphing operators' that represent simple structural changes, such as the addition or removal of an atom or a bond. Molpher incorporates an optimized parallel exploration algorithm, compound logging and a two-dimensional visualization of the exploration process. Its feature set can be easily extended by implementing additional morphing operators, chemical fingerprints, similarity measures and visualization methods. Molpher not only offers an intuitive graphical user interface, but also can be run in batch mode. This enables users to easily incorporate molecular morphing into their existing drug discovery pipelines.
conclusionsMolpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds. These libraries, represented by a morphing path and its surroundings, provide valuable starting data for future in silico and in vitro experiments. Molpher is highly extensible and can be easily incorporated into any existing computational drug design pipeline.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.