ATProto Browser

{
  "text": "Some crystal structures show evidence of multiple stable conformations, such as loops or side chains with two distinct regions of density. These can be correctly modeled by MD, but not modern protein ensemble prediction tools like AlphaFlow or DiG (BioEmu not tested)\n\nwww.biorxiv.org/content/10.1...",
  "$type": "app.bsky.feed.post",
  "embed": {
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    "images": [
      {
        "alt": "Examples of alternate conformations with environmental explanations.\n(A) a protein in two states (open and closed) mediated by allosteric effects; (B) a population of two discrete rotamer states of a sidechain; (C) bound and unbound states due to ligand interaction; (D) different oxidation states of a cysteine pair. Furthermore, some regions in many protein structures exhibit such a degree of flexibility, that no accurate modelling is possible (dashed lines, E). The backbone conformation cannot be determined with crystallographic methods in such cases.",
        "image": {
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          "size": 228052
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        "aspectRatio": {
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        }
      },
      {
        "alt": "Failure of ensemble prediction algorithms in altloc segments.\nAlthough structure and ensemble prediction techniques based on amino acid sequences are capable of accurately reconstructing the overall backbone structure (left column), they consistently fail to produce viable samples corresponding to one of the two altloc conformations (as shown in the magnified regions in the second through fourth columns).",
        "image": {
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          "mimeType": "image/jpeg",
          "size": 575493
        },
        "aspectRatio": {
          "width": 868,
          "height": 1280
        }
      }
    ]
  },
  "langs": [
    "en"
  ],
  "facets": [
    {
      "index": {
        "byteEnd": 300,
        "byteStart": 269
      },
      "features": [
        {
          "uri": "https://www.biorxiv.org/content/10.1101/2024.08.31.610605v1",
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        }
      ]
    }
  ],
  "createdAt": "2025-04-23T14:32:30.355Z"
}