{
  "patent_number": "US 20210174903",
  "country": "US",
  "title": "How to Predict Protein Shapes Better Using Lab Tests and Computers",
  "original_title": "Enhanced protein structure prediction using protein homolog discovery and constrained distograms",
  "summary": "This patent describes a method to improve predicting a protein's 3D shape by combining computer simulations with actual distance measurements from specific parts of the protein in a lab.",
  "what_it_does": "The patent outlines a method for more accurately predicting the three-dimensional structure of a protein. First, it generates a \"multiple sequence alignment\" (MSA) of related proteins (claim 1(i)). A computer then uses this MSA to make an initial guess of the protein's shape, creating a \"distogram\" which is like a map of distances between amino acids (claim 1(ii)). The method then identifies specific amino acids on the protein's surface (claim 1(iii)) and experimentally measures the actual distance between them in a lab, often using a technique called FRET (claim 1(iv), claim 3). These real-world distance measurements are then fed back into the computer model to refine and improve the initial prediction, making it more accurate (claim 1(v)). For example, if the computer initially predicts two surface amino acids are 5 nanometers apart, but the FRET experiment shows they are actually 3 nanometers apart, the computer model is adjusted to reflect the 3 nanometer distance.",
  "what_it_does_not_cover": [
    "Does not cover protein structure prediction methods that rely solely on computational techniques without any in vitro experimental validation.",
    "Does not cover in vitro distance measurements for amino acids that are not solvent-exposed.",
    "Does not cover methods where the experimental distance measurements are not used to constrain or refine the computational prediction algorithm.",
    "Does not cover protein structure prediction that does not involve generating a multiple sequence alignment (MSA) of homologous sequences.",
    "Does not cover methods that do not produce a distogram as an intermediate step in the structure prediction."
  ],
  "filed": "2020-12-10",
  "granted": null,
  "expires": "2040-12-10",
  "status": "active",
  "holder": "Protein Evolution",
  "holder_url": "https://patentbrief.org/company/protein-evolution",
  "inventors": [
    {
      "name": "Jonathan M. Rothberg",
      "url": "https://patentbrief.org/inventor/jonathan-m-rothberg"
    },
    {
      "name": "Brian Reed",
      "url": "https://patentbrief.org/inventor/brian-reed"
    },
    {
      "name": "Eric Kauderer-Abrams",
      "url": "https://patentbrief.org/inventor/eric-kauderer-abrams"
    },
    {
      "name": "Mohammad Moghadamfalahi",
      "url": "https://patentbrief.org/inventor/mohammad-moghadamfalahi"
    },
    {
      "name": "Zhizhuo Zhang",
      "url": "https://patentbrief.org/inventor/zhizhuo-zhang"
    }
  ],
  "times_cited": 21,
  "tags": [
    "biotech",
    "software",
    "ai_ml",
    "pharmaceutical",
    "materials"
  ],
  "abstract": "The present disclosure provides, in some aspects, methods for enhanced protein structure prediction using protein homology discovery and constrained distograms.",
  "url": "https://patentbrief.org/patent/us/20210174903/enhanced-protein-structure-prediction-using-protein-homolog-discovery-and-constr",
  "markdown_url": "https://patentbrief.org/patent/us/20210174903/enhanced-protein-structure-prediction-using-protein-homolog-discovery-and-constr/md",
  "google_patents_url": "https://patents.google.com/patent/US20210174903",
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}