Molecular Modeling By Rashmi Shrivastava Lecturer

Slides:



Advertisements
Similar presentations
PROTEOMICS 3D Structure Prediction. Contents Protein 3D structure. –Basics –PDB –Prediction approaches Protein classification.
Advertisements

Protein Structure Prediction using ROSETTA
Tutorial Homology Modelling. A Brief Introduction to Homology Modeling.
Protein Threading Zhanggroup Overview Background protein structure protein folding and designability Protein threading Current limitations.
Prediction to Protein Structure Fall 2005 CSC 487/687 Computing for Bioinformatics.
Protein Tertiary Structure Prediction
Structural bioinformatics
Structure Prediction. Tertiary protein structure: protein folding Three main approaches: [1] experimental determination (X-ray crystallography, NMR) [2]
Protein Threading Optimization Using Consensus Homology Modeling Maliha Sarwat ( ), Tasmin Tamanna Haque ( ) Department of Computer Science.
CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Homology Modeling Anne Mølgaard, CBS, BioCentrum, DTU.
Tertiary protein structure viewing and prediction July 1, 2009 Learning objectives- Learn how to manipulate protein structures with Deep View software.
Tertiary protein structure viewing and prediction July 5, 2006 Learning objectives- Learn how to manipulate protein structures with Deep View software.
Homology modelling ? X-ray ? NMR ?. Homology Modelling !
Thomas Blicher Center for Biological Sequence Analysis
Summary Protein design seeks to find amino acid sequences which stably fold into specific 3-D structures. Modeling the inherent flexibility of the protein.
The Protein Data Bank (PDB)
. Protein Structure Prediction [Based on Structural Bioinformatics, section VII]
1 Protein Structure Prediction Reporter: Chia-Chang Wang Date: April 1, 2005.
Protein Tertiary Structure. Primary: amino acid linear sequence. Secondary:  -helices, β-sheets and loops. Tertiary: the 3D shape of the fully folded.
Molecular modelling / structure prediction (A computational approach to protein structure) Today: Why bother about proteins/prediction Concepts of molecular.
Protein structure determination & prediction. Tertiary protein structure: protein folding Three main approaches: [1] experimental determination (X-ray.
1 Protein Structure Prediction Charles Yan. 2 Different Levels of Protein Structures The primary structure is the sequence of residues in the polypeptide.
CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Homology Modelling Thomas Blicher Center for Biological Sequence Analysis.
BLOSUM Information Resources Algorithms in Computational Biology Spring 2006 Created by Itai Sharon.
Protein Tertiary Structure Prediction Structural Bioinformatics.
Protein Structures.
Bioinformatics Ayesha M. Khan Spring 2013.
Protein Structure Prediction and Analysis
Homology Modeling David Shiuan Department of Life Science and Institute of Biotechnology National Dong Hwa University.
Protein Tertiary Structure Prediction
Construyendo modelos 3D de proteinas ‘fold recognition / threading’
Development of Bioinformatics and its application on Biotechnology
Practical session 2b Introduction to 3D Modelling and threading 9:30am-10:00am 3D modeling and threading 10:00am-10:30am Analysis of mutations in MYH6.
COMPARATIVE or HOMOLOGY MODELING
CRB Journal Club February 13, 2006 Jenny Gu. Selected for a Reason Residues selected by evolution for a reason, but conservation is not distinguished.
Lecture 10 – protein structure prediction. A protein sequence.
Representations of Molecular Structure: Bonds Only.
Lecture 12 CS5661 Structural Bioinformatics Motivation Concepts Structure Prediction Summary.
De novo Protein Design Presented by Alison Fraser, Christine Lee, Pradhuman Jhala, Corban Rivera.
1 P9 Extra Discussion Slides. Sequence-Structure-Function Relationships Proteins of similar sequences fold into similar structures and perform similar.
Protein Folding Programs By Asım OKUR CSE 549 November 14, 2002.
Protein secondary structure Prediction Why 2 nd Structure prediction? The problem Seq: RPLQGLVLDTQLYGFPGAFDDWERFMRE Pred:CCCCCHHHHHCCCCEEEECCHHHHHHCC.
Applied Bioinformatics Week 12. Bioinformatics & Functional Proteomics How to classify proteins into functional classes? How to compare one proteome with.
Protein Folding and Modeling Carol K. Hall Chemical and Biomolecular Engineering North Carolina State University.
Protein Tertiary Structure. Protein Data Bank (PDB) Contains all known 3D structural data of large biological molecules, mostly proteins and nucleic acids:
Structure prediction: Homology modeling
Protein structure prediction Anttu Kurttio Ville Pietiläinen.
Predicting Protein Structure: Comparative Modeling (homology modeling)
Protein Structure Prediction: Homology Modeling & Threading/Fold Recognition D. Mohanty NII, New Delhi.
Introduction to Protein Structure Prediction BMI/CS 576 Colin Dewey Fall 2008.
Protein Homologue Clustering and Molecular Modeling L. Wang.
BMC Bioinformatics 2005, 6(Suppl 4):S3 Protein Structure Prediction not a trivial matter Strict relation between protein function and structure Gap between.
Query sequence MTYKLILNGKTKGETTTEAVDAATAEKVFQYANDN GVDGEWTYTE Structure-Sequence alignment “Structure is better preserved than sequence” Me! Non-redundant.
Bioinformatics Dipl. Ing. (FH) Patrick Grossmann
Structural classification of Proteins SCOP Classification: consists of a database Family Evolutionarily related with a significant sequence identity Superfamily.
Protein Tertiary Structure Prediction Structural Bioinformatics.
Molecular mechanics Classical physics, treats atoms as spheres Calculations are rapid, even for large molecules Useful for studying conformations Cannot.
Protein Structure Prediction. Protein Sequence Analysis Molecular properties (pH, mol. wt. isoelectric point, hydrophobicity) Secondary Structure Super-secondary.
Homology 3D modeling Miguel Andrade Mainz, Germany Faculty of Biology,
PROTEIN MODELLING Presented by Sadhana S.
Computational Structure Prediction
Protein Structure Prediction and Protein Homology modeling
Protein dynamics Folding/unfolding dynamics
Homology 3D modeling and effect of mutations
Protein dynamics Folding/unfolding dynamics
Protein Structures.
Homology Modeling.
Protein structure prediction.
Protein Homology Modelling
Homology modeling in short…
Presentation transcript:

Molecular Modeling By Rashmi Shrivastava Lecturer School of Biotechnology Devi Ahilya University, Indore

Scope and aim of molecular modeling Accurate prediction of structure from the sequence. To provide the basis of structure- based drug design, analysis of protein functions, interactions, antigenic behavior, rational design of proteins with increased stability or novel function

Methods of Modeling Homology Modeling- The easiest one. Based on the observations that -the structure of protein is uniquely determined by its amino acid sequence. during evolution the structure is more stable and changes at a much slower rate than the associated sequence, So that similar sequences adopt practically identical structures Homology modeling can be used when there is a clear relation (> 30 % identity) between the sequence of a protein of unknown structure to that of a sequence of a known structure, most likely to be found in Protein Data Bank (PDB, a database of solved protein structures).

Threading When there is no recognizable sequence similarity it involves threading a specific sequence through all known folds and, for each fold, estimating the probability that the sequence can have that fold. Threading or the fold recognition approach is based on the fact that apparently unrelated proteins adopt similar folds. To generate sequence- structure alignments 1D-3D profiles are constructed

Ab initio Free energy considerations to obtain low energy minima Conformational space searching It may help in genome wide modeling

Homology Modeling Template selection- BLAST Downloading structure file from PDB Model Building- Modeller Generate atom file- .atm from PDB Generate alignment file- .aln file Generate a script file to give running parameters

Alignment file

Script file in Python

Result files 1fdx.B00001 1fdx.D000001 1fdx.V000001

Model Optimization Select best model- based on conformational features and energy Optimize by minimization of energy Discover CHARMM

Model Validation Use Procheck, ERRAT, VERIFY 3D and energy