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Introduction to
Protein Structure Prediction
BMI/CS 776
www
...
wisc
...
wisc
...
, 1950s]
• but some qualifications
– all proteins can be denatured
– some proteins are inherently disordered (i
...
lack a
regular structure)
– some proteins get folding help from chaperones
– there are various mechanisms through which the
conformation of a protein can be changed in vivo
– post-translational modifications such as
phosphorylation
– prions
– etc
...
g
...
g
...
Rost, “Protein Structure in 1D, 2D, and 3D”, The Encyclopaedia of Computational Chemistry, 1998
Prediction in 3D
• homology modeling
given: a query sequence Q, a database of protein structures
do:
• find protein P such that
– structure of P is known
– P has high sequence similarity to Q
• return P’s structure as an approximation to Q’s
structure
• fold recognition (threading)
given: a query sequence Q, a database of known folds
do:
• find fold F such that Q can be aligned with F in a highly
compatible manner
• return F as an approximation to Q’s structure
Prediction in 3D
• “fragment assembly” (Rosetta)
given: a query sequence Q, a database of structure
fragments
do:
• find a set of fragments that Q can be aligned with in a
highly compatible manner
• return fragment assembly as an approximation to Q’s
structure
• molecular dynamics
given: a query sequence Q
do: use laws of Physics to simulate folding of Q
Prediction in 3D
homology
modeling
threading
fragment assembly
(Rosetta)
molecular
dynamics