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Structure-based drug design (SBDD) refers to designing or optimizing small-molecule ligands that can specifically bind to a pocket, given the known three-dimensional structure of a target protein, by means of molecular docking, scoring functions, and conformational search.
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10/26/2026
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UnverifiedProteins are commonly represented by PDB structures or amino acid sequences, and docking and affinity prediction also require three-dimensional conformation information.63% similarUnverifiedDesignability is a commonly used evaluation criterion in generative protein design: the generated backbone is fed into an independent sequence design model (such as ProteinMPNN), and the predicted sequence is then refolded using a structure prediction tool (such as ESMFold or AlphaFold); if the predicted structure is highly consistent with the original backbone (usually judged by an scRMSD threshold), the backbone is considered designable.59% similarUnverifiedA common combination for landing molecular design is a closed loop of "generative models propose candidates + property models score them + retrosynthesis models assess synthesizability".57% similarUnverifiedThe new protein design framework adopts a de novo design strategy, directly targeting physicochemical properties as the optimization objective rather than homology-based sequence similarity56% similarUnverifiedlDDT is a widely used alignment-free evaluation metric in the field of protein structure prediction and modeling, measuring the agreement of local inter-atomic distances between a predicted structure and a reference structure, with values between 0 and 1, where higher indicates more accurate local geometry.56% similar
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