67 Psiblast PPTs View free & download

From PSIBLAST to HMMer PowerPoint PPT Presentation

From PSIBLAST to HMMer - substitution matrices should be specific to a particular site. ... Same SCOP family based on catalytic domain. Overall structure similarity noted. ACTG ...

substitution matrices should be specific to a particular site. ... Same SCOP family based on catalytic domain. Overall structure similarity noted. ACTG ...

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PsiBLAST, Prosite, UCSC Genome Browser Lecture 3 PowerPoint PPT Presentation

PsiBLAST, Prosite, UCSC Genome Browser Lecture 3 - The challenge is to turn these raw data into biological knowledge ... Profiles are used in prosite when the motif is relatively divergent, and is ...

The challenge is to turn these raw data into biological knowledge ... Profiles are used in prosite when the motif is relatively divergent, and is ...

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Multiple Sequence Alignments PSIBLAST PowerPoint PPT Presentation

Multiple Sequence Alignments PSIBLAST - Identification of conserved, functionally important sites ... Reference: Thompson et al. (1994) Nucleic Acids Res. 22, 4673-4680. 9. Step 1-pairwise alignments ...

Identification of conserved, functionally important sites ... Reference: Thompson et al. (1994) Nucleic Acids Res. 22, 4673-4680. 9. Step 1-pairwise alignments ...

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Protein structure prediction PowerPoint PPT Presentation

Protein structure prediction - PSI-PRED secondary structure prediction based on PSIBLAST ... Strand(E), Helix(H) and Coil(C) AA: RLMPHIKRSAIPVNHGQCRWEDNVDERTNCMIQYVLIMRD ...

PSI-PRED secondary structure prediction based on PSIBLAST ... Strand(E), Helix(H) and Coil(C) AA: RLMPHIKRSAIPVNHGQCRWEDNVDERTNCMIQYVLIMRD ...

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CAP5510 - BLASTP, BLASTN, TBLAST, BLASTX, BLAT, BLASTZ, MegaBLAST, PsiBLAST, PhiBLAST. Others ... BLAT, BLASTZ, MegaBLAST. FLASH, PatternHunter, SSAHA, SENSEI, WABA, ...

BLASTP, BLASTN, TBLAST, BLASTX, BLAT, BLASTZ, MegaBLAST, PsiBLAST, PhiBLAST. Others ... BLAT, BLASTZ, MegaBLAST. FLASH, PatternHunter, SSAHA, SENSEI, WABA, ...

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Sequence Alignment Methods: Dynamic Programming and Heuristic Approaches. PowerPoint PPT Presentation

Sequence Alignment Methods: Dynamic Programming and Heuristic Approaches. - ... PsiBLAST, gap penalties, Smith-Waterman vs. heuristic alignment, repeats ... Local alignment (Smith-Waterman): F(0,0) = 0; F(k,0) = F(0,k) = 0; ...

... PsiBLAST, gap penalties, Smith-Waterman vs. heuristic alignment, repeats ... Local alignment (Smith-Waterman): F(0,0) = 0; F(k,0) = F(0,k) = 0; ...

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Why is pairwise sequence alignment different PowerPoint PPT Presentation

Why is pairwise sequence alignment different - BLASTP 2.2.6 [Apr-09-2003] RID: 1068830459-16741-16367211346.BLASTQ3 ... http://bioweb.pasteur.fr/seqanal/blast/intro-uk.html#psiblast ...

BLASTP 2.2.6 [Apr-09-2003] RID: 1068830459-16741-16367211346.BLASTQ3 ... http://bioweb.pasteur.fr/seqanal/blast/intro-uk.html#psiblast ...

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Demystifying sequence number four PowerPoint PPT Presentation

Demystifying sequence number four - Aart, a six finger zinc finger designed to recognize ann triplets. PSIBLAST. Zebra fish (danio rerio) - similar to Zinc finger protein ...

Aart, a six finger zinc finger designed to recognize ann triplets. PSIBLAST. Zebra fish (danio rerio) - similar to Zinc finger protein ...

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Stand alone BLAST on Linux PowerPoint PPT Presentation

Stand alone BLAST on Linux - Unzip the distribution. Helpful info: Standalone BLAST is ... Unzip the swissprot database. View the contents of the swissprot database. FASTA format ...

Unzip the distribution. Helpful info: Standalone BLAST is ... Unzip the swissprot database. View the contents of the swissprot database. FASTA format ...

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Bioinformatics is a Field of a Distributed Knowledge: Databases and Servers. PowerPoint PPT Presentation

Bioinformatics is a Field of a Distributed Knowledge: Databases and Servers. - SCOP: up to 7 folds per function and up to 15 functions per fold ... SCOP (Structural Classification of Proteins, scop.berkeley.edu, Murzin et. al. ...

SCOP: up to 7 folds per function and up to 15 functions per fold ... SCOP (Structural Classification of Proteins, scop.berkeley.edu, Murzin et. al. ...

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Computer-aided Drug Discovery G.P.S. Raghava PowerPoint PPT Presentation

Computer-aided Drug Discovery G.P.S. Raghava - Drug. Informatics. Searching and analyzing ... Nucleic Acids Research 2004, 32:W414-9. HSLpred: Sub cellular localization ... Nucleic Acids Research 33:W154-9 ...

Drug. Informatics. Searching and analyzing ... Nucleic Acids Research 2004, 32:W414-9. HSLpred: Sub cellular localization ... Nucleic Acids Research 33:W154-9 ...

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Protein Secondary Structure Prediction C606 Paper presentation PowerPoint PPT Presentation

Protein Secondary Structure Prediction C606 Paper presentation - A Two-stage Classifier for Protein -turn Prediction using Support Vector Machines ... Predicting -turns -turns are a type of coil. Frequent. Important in ...

A Two-stage Classifier for Protein -turn Prediction using Support Vector Machines ... Predicting -turns -turns are a type of coil. Frequent. Important in ...

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Predicting Protein Structure: PowerPoint PPT Presentation

Predicting Protein Structure: - Predicting Protein Structure: Comparative Modeling (homology modeling)

Predicting Protein Structure: Comparative Modeling (homology modeling)

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Biological Networks - Biological Networks

Biological Networks

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Entropy, Information contents PowerPoint PPT Presentation

Entropy, Information contents - ... Definition Entropy of random variable is a measure of the uncertainty In Thermodynamics G=H-T S The entropy S of a system is the degree of disorder ...

... Definition Entropy of random variable is a measure of the uncertainty In Thermodynamics G=H-T S The entropy S of a system is the degree of disorder ...

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Bioinformatics is a Field of a Distributed Knowledge: Databases and Servers' - ... (connectivity of secondary structures e.g. globin-like, Rossman fold); 1846 ... Live Bench evaluation (http://BioInfo.PL/LiveBench/1 ...

... (connectivity of secondary structures e.g. globin-like, Rossman fold); 1846 ... Live Bench evaluation (http://BioInfo.PL/LiveBench/1 ...

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MCB 372 - MCB 372 PSI BLAST, scalars J. Peter Gogarten Office: BPB 404 phone: 860 486-4061, Email: gogarten@uconn.edu

MCB 372 PSI BLAST, scalars J. Peter Gogarten Office: BPB 404 phone: 860 486-4061, Email: gogarten@uconn.edu

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Introduction to the GCG Wisconsin Package PowerPoint PPT Presentation

Introduction to the GCG Wisconsin Package - Introduction to the GCG Wisconsin Package The Center for Bioinformatics UNC at Chapel Hill Jianping (JP) Jin Ph.D. Bioinformatics Scientist Phone: (919)843-6105

Introduction to the GCG Wisconsin Package The Center for Bioinformatics UNC at Chapel Hill Jianping (JP) Jin Ph.D. Bioinformatics Scientist Phone: (919)843-6105

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Sequence Alignment Methods: Dynamic Programming and Heuristic Approaches. - There is one-to-one correspondence (bijection) between the set of non-redundant ... past that led to it through one (most favorable together with the cost of the ...

There is one-to-one correspondence (bijection) between the set of non-redundant ... past that led to it through one (most favorable together with the cost of the ...

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Workflows - HoneyBee genome. The MotifNetwork is a suite of workflows. Generation of new data and techniques ... wide comprehensive analysis on the recent honey bee genome ...

HoneyBee genome. The MotifNetwork is a suite of workflows. Generation of new data and techniques ... wide comprehensive analysis on the recent honey bee genome ...

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Computational Short Cuts to Protein Structure and Function: Fold Recognition Methods. PowerPoint PPT Presentation

Computational Short Cuts to Protein Structure and Function: Fold Recognition Methods. - SCOP: up to 7 folds per function and up to 15 functions per fold ... SCOP (Structural Classification of Proteins, scop.berkeley.edu, Murzin et. al. ...

SCOP: up to 7 folds per function and up to 15 functions per fold ... SCOP (Structural Classification of Proteins, scop.berkeley.edu, Murzin et. al. ...

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Protein Secondary Structure Prediction PowerPoint PPT Presentation

Protein Secondary Structure Prediction - 8 11 A E E A 19 0A 63 -2,-0.4 2,-0.3 11,-0.2 11,-0.2 -0.933 4.4 175.4-139.1 156. ... Assumes amino acids up to 8 residues on each side influence the ss of the ...

8 11 A E E A 19 0A 63 -2,-0.4 2,-0.3 11,-0.2 11,-0.2 -0.933 4.4 175.4-139.1 156. ... Assumes amino acids up to 8 residues on each side influence the ss of the ...

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MICa 8006 Protein Sequence Analysis PowerPoint PPT Presentation

MICa 8006 Protein Sequence Analysis - Smith-Waterman: 'optimal', slow. Blast, Fasta: not guaranteed optimal; faster. wxyzabcdef j ... Smith - Waterman: local. Both are slow, but 'optimal' ...

Smith-Waterman: 'optimal', slow. Blast, Fasta: not guaranteed optimal; faster. wxyzabcdef j ... Smith - Waterman: local. Both are slow, but 'optimal' ...

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Protein modelling PowerPoint PPT Presentation

Protein modelling - Protein structure determines ... Chothia & Lesk (1986): Correlation between structural divergence and ... Fold prediction Rosetta method. Knowledge based ...

Protein structure determines ... Chothia & Lesk (1986): Correlation between structural divergence and ... Fold prediction Rosetta method. Knowledge based ...

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Where do you go from a protein sequence: PowerPoint PPT Presentation

Where do you go from a protein sequence: - Components E1 to E5 Physical chemical Properties ... PCPMer to profile sequences according to physical chemical property based motifs. ...

Components E1 to E5 Physical chemical Properties ... PCPMer to profile sequences according to physical chemical property based motifs. ...

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Introduction to Bioinformatics: Lecture XI Computational Protein Structure Prediction PowerPoint PPT Presentation

Introduction to Bioinformatics: Lecture XI Computational Protein Structure Prediction - Multiple sequence alignment and family profiles. Secondary structure and solvent ... membrane regions based on 'hydropathy' (or hydrophobicity) profiles. ...

Multiple sequence alignment and family profiles. Secondary structure and solvent ... membrane regions based on 'hydropathy' (or hydrophobicity) profiles. ...

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PREDICTING PROTEIN SECONDARY STRUCTURE USING ARTIFICIAL NEURAL NETWORKS PowerPoint PPT Presentation

PREDICTING PROTEIN SECONDARY STRUCTURE USING ARTIFICIAL NEURAL NETWORKS - Title: PowerPoint Presentation Author: Valued Sony Customer Last modified by: njit Created Date: 4/29/2002 1:34:55 AM Document presentation format

Title: PowerPoint Presentation Author: Valued Sony Customer Last modified by: njit Created Date: 4/29/2002 1:34:55 AM Document presentation format

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The structure and assembly process of the SV40 virus shell PowerPoint PPT Presentation

The structure and assembly process of the SV40 virus shell - Determine the type of bond according to the distance and type of atoms: ... Bond, James Bond. Electrostatic: opposite electric charges. ?G 5 kcal/mol. Hydrogen: ...

Determine the type of bond according to the distance and type of atoms: ... Bond, James Bond. Electrostatic: opposite electric charges. ?G 5 kcal/mol. Hydrogen: ...

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Basics of Sequence Alignment and Weight Matrices and DOT Plot PowerPoint PPT Presentation

Basics of Sequence Alignment and Weight Matrices and DOT Plot - Basics of Sequence Alignment and Weight Matrices and DOT Plot G P S Raghava Email: raghava@imtech.res.in Web: http://imtech.res.in/raghava/

Basics of Sequence Alignment and Weight Matrices and DOT Plot G P S Raghava Email: raghava@imtech.res.in Web: http://imtech.res.in/raghava/

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Techniques for Protein Sequence Alignment and Database Searching PowerPoint PPT Presentation

Techniques for Protein Sequence Alignment and Database Searching - Techniques for Protein Sequence Alignment and Database Searching. G P S Raghava ... Fitch 1966 based on Nucleotide Base change required (0,1,2,3) ...

Techniques for Protein Sequence Alignment and Database Searching. G P S Raghava ... Fitch 1966 based on Nucleotide Base change required (0,1,2,3) ...

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Computeraided Vaccine and Drug Discovery G'P'S' Raghava PowerPoint PPT Presentation

Computeraided Vaccine and Drug Discovery G'P'S' Raghava - Drug Informatics. 2. Limitations of methods of subunit vaccine design ... Bhasin and Raghava (2005) Nucleic Acids Research 33: W202-7 ...

Drug Informatics. 2. Limitations of methods of subunit vaccine design ... Bhasin and Raghava (2005) Nucleic Acids Research 33: W202-7 ...

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Pair-wise and Multiple Sequence Alignment Using Dynamic Programming (Local PowerPoint PPT Presentation

Pair-wise and Multiple Sequence Alignment Using Dynamic Programming (Local - Pair-wise and Multiple Sequence Alignment Using Dynamic Programming (Local & Global Alignment) ... of Two Sequences (Pair-wise Alignment) The Scoring Schemes or ...

Pair-wise and Multiple Sequence Alignment Using Dynamic Programming (Local & Global Alignment) ... of Two Sequences (Pair-wise Alignment) The Scoring Schemes or ...

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Various Career Options Available PowerPoint PPT Presentation

Various Career Options Available - first aligning the most similar pair of sequences ... Repeats and calculate significance (t-test) Significance of fold used statistical method ...

first aligning the most similar pair of sequences ... Repeats and calculate significance (t-test) Significance of fold used statistical method ...

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Protein Classification PowerPoint PPT Presentation

Protein Classification - Protein Classification PDB Growth Protein classification Number of protein sequences grow exponentially Number of solved structures grow exponentially Number of new ...

Protein Classification PDB Growth Protein classification Number of protein sequences grow exponentially Number of solved structures grow exponentially Number of new ...

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Classifying the protein universe PowerPoint PPT Presentation

Classifying the protein universe - Protein families are defined by homology: In a family, everyone is related to everyone ... describes essential features of the protein family ...

Protein families are defined by homology: In a family, everyone is related to everyone ... describes essential features of the protein family ...

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Various Career Options Available - SRF: Spectral Repeat Finder (SRF) is a program to find repeats through an ... also launched by European Bioinformatics Institute (EBI) Hinxton, Cambridge, UK. ...

SRF: Spectral Repeat Finder (SRF) is a program to find repeats through an ... also launched by European Bioinformatics Institute (EBI) Hinxton, Cambridge, UK. ...

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Homology Modeling PowerPoint PPT Presentation

Homology Modeling - Homology Modeling Homology Modeling Presentation Fold recognition Model building Loop building Sidechain modeling Refinement Testing methods: the CASP experiment ...

Homology Modeling Homology Modeling Presentation Fold recognition Model building Loop building Sidechain modeling Refinement Testing methods: the CASP experiment ...

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Machine Learning for Protein Classification: Kernel Methods PowerPoint PPT Presentation

Machine Learning for Protein Classification: Kernel Methods - MACHINE LEARNING FOR PROTEIN CLASSIFICATION ... Kernel Methods Outline Proteins The Protein Problem How to look at amino acid chains Families ...

MACHINE LEARNING FOR PROTEIN CLASSIFICATION ... Kernel Methods Outline Proteins The Protein Problem How to look at amino acid chains Families ...

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Introduction to Bioinformatics: Lecture XI Computational Protein Structure Prediction - Introduction to Bioinformatics: Lecture XI Computational Protein Structure Prediction Jarek Meller Division of Biomedical Informatics, Children s Hospital Research ...

Introduction to Bioinformatics: Lecture XI Computational Protein Structure Prediction Jarek Meller Division of Biomedical Informatics, Children s Hospital Research ...

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Sequence Similarity PowerPoint PPT Presentation

PSI-BLAST. Given a sequence query x, and database D ... BLAST Variants. BLASTN genomic sequences. BLASTP proteins ... Score of the global map is maximum ...

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Protein Classification - Detect similarities (evolutionary relationships) between protein sequences ... www.biochem.ucl.ac.uk/bsm/cath. FSSP. Automatic classification (L. Holm) ...

Detect similarities (evolutionary relationships) between protein sequences ... www.biochem.ucl.ac.uk/bsm/cath. FSSP. Automatic classification (L. Holm) ...

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I keep six honest serving-men (They taught me all I knew); PowerPoint PPT Presentation

I keep six honest serving-men (They taught me all I knew); - I keep six honest serving-men (They taught me all I knew); Their names are What , and Why, and When, And How, and Where, and ...

I keep six honest serving-men (They taught me all I knew); Their names are What , and Why, and When, And How, and Where, and ...

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Basics of Sequence Alignment and Weight Matrices and DOT Plot - Basics of Sequence Alignment and Weight Matrices and DOT Plot G P S Raghava Email: raghava@imtech.res.in Web: http://imtech.res.in/raghava/ Importance of Sequence ...

Basics of Sequence Alignment and Weight Matrices and DOT Plot G P S Raghava Email: raghava@imtech.res.in Web: http://imtech.res.in/raghava/ Importance of Sequence ...

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Presentacin de PowerPoint PowerPoint PPT Presentation

Presentacin de PowerPoint - An EU-US Course in Environmental Biotechnology. H. influenza. http://www.rcsb.org/pdb ... Identities = 183/305 (60%), Positives = 233/305 (76%), Gaps = 1/305 (0 ...

An EU-US Course in Environmental Biotechnology. H. influenza. http://www.rcsb.org/pdb ... Identities = 183/305 (60%), Positives = 233/305 (76%), Gaps = 1/305 (0 ...

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PREDICTING PROTEIN SECONDARY STRUCTURE USING ARTIFICIAL NEURAL NETWORKS - Chrissy Oriol. Lydia Shih. Sudhakar Reddy. Proteins. And Secondary Structure. Project Goals ... CHRISSY ORIOL. JNET AND JPRED. Multiple Alignement. Neural ...

Chrissy Oriol. Lydia Shih. Sudhakar Reddy. Proteins. And Secondary Structure. Project Goals ... CHRISSY ORIOL. JNET AND JPRED. Multiple Alignement. Neural ...

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Protein Structure Prediction - Bioinformatics Centre. Institute of Microbial Technology Chandigarh, INDIA ... Kaur and Raghava (2002) J. Bioinformatics and Computational Biology, 1:495:504 ...

Bioinformatics Centre. Institute of Microbial Technology Chandigarh, INDIA ... Kaur and Raghava (2002) J. Bioinformatics and Computational Biology, 1:495:504 ...

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Structural bioinformatics for glycobiology PowerPoint PPT Presentation

Structural bioinformatics for glycobiology - The

The

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the Blat Rap PowerPoint PPT Presentation

the Blat Rap - 10 billion bases of genome, more to come. 15 million ... Smith-Waterman technique based on dynamic programming. 'Banded' Smith-Waterman: faster but doesn't ...

10 billion bases of genome, more to come. 15 million ... Smith-Waterman technique based on dynamic programming. 'Banded' Smith-Waterman: faster but doesn't ...

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Some Computer Science Techniques in Bioinformatics PowerPoint PPT Presentation

Some Computer Science Techniques in Bioinformatics - Less amenable to rigid rule-based algorithms. ... on tyrosine when associated to the TCR zeta chain and was able to bind p56(lck) ...

Less amenable to rigid rule-based algorithms. ... on tyrosine when associated to the TCR zeta chain and was able to bind p56(lck) ...

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MrBUMP Molecular Replacement with Bulk Model Preparation PowerPoint PPT Presentation

MrBUMP Molecular Replacement with Bulk Model Preparation - An automation framework for Molecular Replacement. ... The resulting models from molecular replacement are passed to Refmac for restrained refinement. ...

An automation framework for Molecular Replacement. ... The resulting models from molecular replacement are passed to Refmac for restrained refinement. ...

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Protein Structure Prediction - ... free energy of protein surface. Knowledge Based approaches ... atoms in protein is in static ... Blast search against protein sequence (NR) Multiple ...

... free energy of protein surface. Knowledge Based approaches ... atoms in protein is in static ... Blast search against protein sequence (NR) Multiple ...

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Computer Programs for Biological Problems: Is it Service or Science G. P. S. Raghava PowerPoint PPT Presentation

Computer Programs for Biological Problems: Is it Service or Science G. P. S. Raghava - Computer Programs for Biological Problems: Is it Service or Science ? G. P. S. Raghava ... Participate in all competitions like EVA, CAFASP and CASP (In top 5 methods) ...

Computer Programs for Biological Problems: Is it Service or Science ? G. P. S. Raghava ... Participate in all competitions like EVA, CAFASP and CASP (In top 5 methods) ...

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Structure prediction PowerPoint PPT Presentation

Structure prediction - 4 Basic Levels of Protein Structure and all information is in the sequence ... AB-INITIO methods. Simulate the process of folding ...

4 Basic Levels of Protein Structure and all information is in the sequence ... AB-INITIO methods. Simulate the process of folding ...

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Rosetta on the Biowulf Cluster - Rosetta on the Biowulf Cluster

Rosetta on the Biowulf Cluster

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Knowledgebased protocols for protein structure prediction: from protein threading to solvent accessi - Knowledgebased protocols for protein structure prediction: from protein threading to solvent accessi

Knowledgebased protocols for protein structure prediction: from protein threading to solvent accessi

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Introduction to Bioinformatics PowerPoint PPT Presentation

Introduction to Bioinformatics - Profile Methods. Structure Prediction. Sequence alignments can be used to infer homology ... Bos taurus (Bovine) Homo sapiens (Human) ORGANISM. Orphan G ...

Profile Methods. Structure Prediction. Sequence alignments can be used to infer homology ... Bos taurus (Bovine) Homo sapiens (Human) ORGANISM. Orphan G ...

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Psiblast PowerPoint PPT Presentations