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.