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US 2021/0174893 A1Published application
Protein structure prediction
AssigneeHomodeus, Inc.
InventorsBenjamin Rosenbluth, Brian Reed, Jonathan M. Rothberg
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Abstract
The present disclosure provides, in some aspects, methods for using FRET-based distance measurements to refine and constrain protein structure prediction algorithms.
Claims20
A method comprising:
- (i) performing in silico a three-dimensional structure prediction of a protein using a structure prediction algorithm;
- (ii) identifying in silico at least one pair of solvent-exposed amino acids in the protein, based on at least one algorithm-predicted factor;
- (iii) labeling in vitro the at least one pair of amino acids in at least one recombinant copy of the protein such that a fluorescence resonance energy transfer (FRET) donor is attached to the first amino acid of the pair and a FRET acceptor is attached to the second amino acid of the pair;
- (iv) collecting in vitro distance measurements between the two amino acids of the at least one pair using FRET;
- and
- (v) constraining the structure prediction algorithm using the collected distance measurements.
3 more elements
A computer-implemented method comprising:
- performing in silico a three-dimensional structure prediction of a protein using a structure prediction algorithm;
- identifying in silico at least one pair of solvent-exposed amino acids in the protein based on at least one algorithm-predicted factors;
- and
- constraining the structure prediction algorithm using distance measurements collected in vitro between amino acids of the at least one pair of amino acids present in a recombinant copy of the protein using fluorescence resonance energy transfer (FRET), wherein a FRET donor is attached to one amino acid of the pair and a FRET acceptor is attached to the other amino acid of the pair.
1 more element
A computer readable medium on which is stored a computer program which, when implemented by a computer processor, causes the processor to:
- perform in silico a three-dimensional structure prediction of a protein using a structure prediction algorithm;
- identify in silico at least one pair of solvent-exposed amino acids in the protein based on at least one algorithm-predicted factor;
- and
- constrain the structure prediction algorithm using distance measurements collected in vitro between amino acids of the at least one pair of amino acids present in a recombinant copy of the protein using fluorescence resonance energy transfer (FRET), wherein a FRET donor is attached to one amino acid of the pair and a FRET acceptor is attached to the other amino acid of the pair.
1 more element
Dependencies are inferred from the claim text.