PPT-Protein Structure Prediction

Why do we want to know protein structure Classification Functional Prediction What is protein structure Primary chains of amino acids Secondary interaction between groups of amino acids Tertiary the organization in three dimensions of all the atoms in a polypeptide. What can we compare?. 3D shapes (RMSD). Atomic motions (B-value, RMSF). Solvent accessibilities (SASA). AMIGOS - Reads an RNA PDB file and outputs a complete table of torsion angle calculations.. APBS - Software for evaluating the electrostatic properties of . 45 Workshop # 7 : Docking Protein – components . The search space can be extremely large, so large amounts of computational resources are typically required . In this workshop, we will explo Beyond protein structure. Miguel . Andrade. Faculty of Biology, . Johannes Gutenberg University . Institute of Molecular Biology. Mainz, Germany. a. ndrade@uni-mainz.de. Transmembrane helices. N-terminal signals. Avdesh Mishra, . Md. . Tamjidul. . Hoque. {amishra2, . thoque. }@uno.edu. Presented By: Avdesh Mishra. Department of Computer Science. Protein structure in its native state gains lowest free energy. Miguel . Andrade. Faculty of Biology, . Johannes Gutenberg University . Institute of Molecular Biology. Mainz, Germany. a. ndrade@uni-mainz.de. X-ray crystallography . (103,988 . in PDB). need crystals. Advisor: Dr. Chen . Keasar. Arie Barsky, Nadav Nuni. Protein folding problem. Proteins are responsible for constructing and operating the organism, and are made of chains of amino-acids. Protein folding problem. przewidywania struktury białek Magdalena Mozolewska Instytut Podstaw Informatyki PAN Importance • In most cases function of the proteins depends strictly on their structure: • denatured enzymes VBC-603. P.G.. 30.12.2020. Protein . Strucuture. Sequence, Structure and Function. What determines fold?. Anfinsen’s experiments in 1957 demonstrated that proteins can fold spontaneously into their native conformations under physiological conditions. This implies that primary structure does indeed determine folding or 3-D . . Miguel . Andrade. Faculty of Biology, . Johannes Gutenberg University . Institute of Molecular Biology. Mainz, Germany. a. ndrade@uni-mainz.de. Secondary structure prediction. Amino acid sequence -> Secondary structure. computer science, mathematics, information technology and statistics. to analyze the biological data like . genomics, Protein structure prediction, . Pharmaco-phore. modeling , toxicity prediction and drug designing.. VBC-603. P.G.. 02.01.2021. Knowledge Based Approaches. Homology Modelling. Need homologues of known protein structure. Backbone modelling. Side chain modelling . Fail in absence of homology. Threading Based Methods. Prediction . Wang Yang. 2014.1.3. Outline. Molecular. . Co-evolution . phenomenon. A. pplications . of Co-evolution . in . protein structure prediction and PPI prediction.. Co-evolution measurement: . Some of the slides are adapted from Dr. Dong Xu’s lecture notes. Why secondary structure prediction?. Accurate secondary structure prediction can be an important information for the tertiary structure prediction. Secondary structures. Tertiary structures. MTYKLILNGKTKGETTTEAVDAATAEKVFQYANDNGVDGEWTYTE. helices. strands. loops. Three dimensional packing of secondary structures. Protein Structures. Protein structures.