RDKit
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Related Articles from SNS
The Geometry of Activity Cliffs: Representation Dependence and Multi-Scale Characterization of Activity Landscapes
Announce Type: cross Abstract: Activity cliffs, structurally similar compounds with large potency differences, are widely treated as intrinsic features of chemical datasets. We argue that apart from target biology, much of our cliff understanding is a consequence of the geometry induced by the chosen molecular representation, not a property of a molecule pair itself. We designed a six-step pipeline to systematically test this hypothesis.
The Geometry of Activity Cliffs: Representation Dependence and Multi-Scale Characterization of Activity Landscapes
Announce Type: cross Abstract: Activity cliffs, structurally similar compounds with large potency differences, are widely treated as intrinsic features of chemical datasets. We argue that apart from target biology, much of our cliff understanding is a consequence of the geometry induced by the chosen molecular representation, not a property of a molecule pair itself. We designed a six-step pipeline to systematically test this hypothesis.
Fast Organic Crystal Structure Prediction with Unit Cell Flow Matching
arXiv:2606.03199v1 Announce Type: new Abstract: Organic crystal structure prediction (CSP) is a requirement for computational modelling of organic solids, but traditionally costs several CPU-years per molecule. Generative models such as OXtal dramatically reduce this cost by sampling stable organic crystal structures directly. However, OXtal forgoes explicit lattice parametrization in favour of modelling large crops of the bulk material with expensive triangle layers, which can incur a...
Fast Organic Crystal Structure Prediction with Unit Cell Flow Matching
arXiv:2606.03199v1 Announce Type: cross Abstract: Organic crystal structure prediction (CSP) is a requirement for computational modelling of organic solids, but traditionally costs several CPU-years per molecule. Generative models such as OXtal dramatically reduce this cost by sampling stable organic crystal structures directly. However, OXtal forgoes explicit lattice parametrization in favour of modelling large crops of the bulk material with expensive triangle layers, which can incur a...
Agentic Molecular Recovery via Molecule-Aware Exploration
arXiv:2606.05847v1 Announce Type: new Abstract: Text-guided molecular generation with LLMs often yields invalid SMILES. We argue that invalid drafts should be addressed through a shift from validity-oriented repair to identity-preserving molecular recovery: the objective is not only to restore chemical validity, but also to preserve target-relevant structural cues and recover the molecular identity implied by the description. This perspective reveals the limitations of existing correction...