Modularity of Protein Folds as a Tool for
Template-Free Modeling of StructuresBrinda Vallat, Carlos Madrid-Aliste, Andras Fiser
Department of Systems and Computational Biology, Albert Einstein College of Medicine,
Bronx, New York, USA
Presentation by
Pranavathiyani GM.Sc Bioinformatics
Centre for Bioinformatics
Pondicherry University
IF 4.829
Introduction
Proteins are made up of amino
acids.
Protein Structural Organization.
i) Primary
ii) Secondary
iii)Tertiary
iv)Quaternary
Each protein folds into a unique
three-dimensional structure that
enables it to carry out its
biological function.
Predicting the 3D structure of proteins from their amino acid sequences remains a challenging problem.
Sequence-Structure-Function Relation
Structure Prediction methods
Computational protein structure prediction
Comparative modelling
Fragment assembly based methods
Fragment assembly based methods use a library of protein fragments
obtained from known protein structures to explore the structure space
accessible to the query protein.
The fragments themselves may be obtained from remote homologs that
share very weak sequence similarity with the query protein and are
typically not good enough to be used directly for homology modelling.
The quality of prediction drops significantly for larger proteins since
the conformational search becomes tedious and less accurate for larger
proteins.
Flowchart of the SmotifTF prediction algorithm.
GDT_TS values of top scoring models obtained with SmotifTF
method using dynamic Smotif library generated at different e-value
cutoffs.
Performance of SmotifTF on the benchmarking test set in
comparison to other methods
Factors affecting model quality
Secondary structure prediction method
Size of the protein.
Smotif ranking using HHalign.
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