Protein Structure Prediction Alignment

May 13, 2013

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??????. ????????????????????????????????????. Bioinformatics. Human Genome ProjectLarge molecule data in biology, such as DNA and proteinKnowledge of mathematics, computer science, information science, physics, system science, management science as well as biologyGenomics (????)DNA sequencingGene predictionSequence alignment.

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Protein Structure Prediction Alignment

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Protein structure prediction

Protein structure prediction. Alexander Churbanov University of Nebraska at Omaha CSCI 8980 February 14, 2002. Structure of the presentation. Introduction Protein native structure Computational methods of finding a native structure Common methods and principles Specific methods

1.02k views • 39 slides

Protein Structure Prediction

Protein Structure Prediction. Protein Sequence +. Dr. G.P.S. Raghava. Structure. Protein Structure Prediction. Experimental Techniques X-ray Crystallography NMR Limitations of Current Experimental Techniques Protein DataBank (PDB) -> 23000 protein structures

963 views • 34 slides

Protein structure prediction

Protein structure prediction. May 24, 2005 Return of Quiz#3 Writing assignments-please hand in.

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Protein Structure Prediction

Protein Structure Prediction. Samantha Chui Oct. 26, 2004. DNA sequence. Protein sequence. Protein structure. transcription & translation. folding. Central Dogma of Biology. Question: Given a protein sequence, to what conformation will it fold?. How does nature do it?.

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Protein Structure Prediction

Protein Structure Prediction. Protein Secondary Structure Prediction. Refers to the prediction of the conformational state of each amino acid residue of a protein sequence as one of the 3 possible states – helices, strands or coils. Methods

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Protein structure prediction

Protein structure prediction. May 26, 2011 HW #8 due today Quiz #3 on Tuesday, May 31

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Protein Structure Prediction

Protein Structure Prediction. Historical Perspective. Protein Folding: From the Levinthal Paradox to Structure Prediction, Barry Honig, 1999 A personal perspective on advances and developments in protein folding over the last 40 years. Levinthal Paradox.

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Protein Structure Prediction

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

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Protein structure prediction

Protein structure prediction. “Protein Threading”. The time required to find the global minimum is shown on log-log axes as a function of search space size. “Global Optimum Protein Threading with Gapped Alignment and Empirical Pair Score Functions” Lathrop and Smith

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Protein Structure Prediction

Protein Structure Prediction. Mason Bially. Types of Structure. Primary Structure The linear amino acid sequence. Secondary Structure The local three-dimensional structure. Defined by hydrogen bonding patterns. Tertiary Structure The global three-dimensional structure.

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Protein structure prediction

Protein structure prediction. Scoring matrices workshop review

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Protein Structure Prediction

Protein Structure Prediction. What is PSP ?. Primary sequence (1D). Tertiary Structure (3D). …ACLLYYTTCAT…. all bonds angles , dihedral angles and bond lengths between each amino acid residue in protein. “Solving” PSP. View PSP as a search.

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Protein Structure Prediction

Protein Structure Prediction. What’s the big deal? Why is it important? Who is working on it Different methods. Methods; Comparative modeling Fold recognition or threading ab initio folding Genetic algorthms. Why do we need structure prediction?.

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Protein Structure Prediction

Protein Structure Prediction. Why ? Type of protein structure predictions Sec Str. Pred Homology Modelling Fold Recognition Ab Initio Secondary structure prediction Why History Performance Usefullness. Why do we need structure prediction?. 3D structure give clues to function:

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Protein Structure Prediction

Protein Structure Prediction. Reporter: Chia-Chang Wang Date: April 1, 2005. Introduction. Why do we need protein structure prediction  X-ray Crystallography, Nuclear Magnetic Resource(NMR) and Molecular Dynamics(MD)

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Protein structure prediction

Protein structure prediction. May 15, 2001 Quiz#4 postponed Writing assignment Learning objectives-Understand the basis of secondary structure prediction programs. Understand neural networks. Become familiar with manipulating known protein structures with Cn3D.

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Protein structure prediction

Protein structure prediction. Homology-based methods. Reading. Required reading for this week David Baker and Andrej Sali, “Protein Structure Prediction and Structural Genomics” Science 2001 Pevsner, Ch. 11 (Protein Structure; note addition to syllabus) Additional sources for this lecture:

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Protein Structure Prediction

Protein Structure Prediction. Xiaole Shirley Liu And Jun Liu STAT115. Protein Structure Prediction Ram Samudrala University of Washington. Outline. Motivations and introduction Protein 2 nd structure prediction Protein 3D structure prediction CASP Homology modeling Fold recognition

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Protein structure prediction

Protein data bank (PDB) : 46818 structures (oct 2007) SCOP (Structural Classification Of Proteins): • 971 folds (major structural similarity) • 1586 super-families (probable common evolutionary origin) • 3004 families (clear evolutionary relationship, ~ 30% identity).

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Protein Structure Prediction

Protein Structure Prediction. BMI/CS 776 www.biostat.wisc.edu/~craven/776.html Mark Craven craven@biostat.wisc.edu April 2002. The Protein Folding Problem. we know that the function of a protein is determined by its 3D shape ( fold , conformation )

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Protein Structure Prediction

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Protein Structure Prediction

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