147 Rotamers PPTs View free & download

Using Pseudotorsions to Predict the Consensus Rotamers - Using Pseudotorsions to Predict the Consensus Rotamers

Using Pseudotorsions to Predict the Consensus Rotamers

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Crystallographic RNA model building using backbone rotamers PowerPoint PPT Presentation

Crystallographic RNA model building using backbone rotamers - Crystallographic RNA model building using backbone rotamers. Kevin Keating. Pyle lab, Yale University. RNA Crystallography. RNA backbone rotamers ...

Crystallographic RNA model building using backbone rotamers. Kevin Keating. Pyle lab, Yale University. RNA Crystallography. RNA backbone rotamers ...

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Basics of protein structure and stability IV: Anatomy of protein structure continued PowerPoint PPT Presentation

Basics of protein structure and stability IV: Anatomy of protein structure continued - X-ray structures of proteins do not in general include hydrogen atom coordinates ... its t rotamer (picture at right) distribution of. valine rotamers. in ...

X-ray structures of proteins do not in general include hydrogen atom coordinates ... its t rotamer (picture at right) distribution of. valine rotamers. in ...

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Gene Ontology (GO) PowerPoint PPT Presentation

Gene Ontology (GO) - Title: Gene Ontology (GO) Author: Victor A Simossis Last modified by: heringa Created Date: 2/3/2004 12:07:02 PM Document presentation format: On-screen Show (4:3)

Title: Gene Ontology (GO) Author: Victor A Simossis Last modified by: heringa Created Date: 2/3/2004 12:07:02 PM Document presentation format: On-screen Show (4:3)

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Gene Ontology (GO) - C E N T R F O R I N T E G R A T I V E E B I O I N F O R M A T I C S V U Bioinformatics Master Course DNA/Protein Structure-function Analysis and Prediction Lecture 10 ...

C E N T R F O R I N T E G R A T I V E E B I O I N F O R M A T I C S V U Bioinformatics Master Course DNA/Protein Structure-function Analysis and Prediction Lecture 10 ...

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Gene Ontology (GO) - remove side chains whose position may be in doubt using a number of filters, ... Modelling new IgM structure using two templates and an antigen (peptide ligand) ...

remove side chains whose position may be in doubt using a number of filters, ... Modelling new IgM structure using two templates and an antigen (peptide ligand) ...

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Sidechain Placement and Protein Design PowerPoint PPT Presentation

Sidechain Placement and Protein Design - Ribose. YPVDLKLVVKQ binding protein. Modify sequence TNT. to change structure binding ... Side chain angles are defined moving outward from the backbone, starting ...

Ribose. YPVDLKLVVKQ binding protein. Modify sequence TNT. to change structure binding ... Side chain angles are defined moving outward from the backbone, starting ...

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Homology modelling PowerPoint PPT Presentation

Homology modelling - Two aligned proteins' The 8' Steps of Modelling. 1 Detect template. 2 Get alignment ... Keep only model and template. How to align: ASASASASASAS. YPYPYPYPYPYP ...

Two aligned proteins' The 8' Steps of Modelling. 1 Detect template. 2 Get alignment ... Keep only model and template. How to align: ASASASASASAS. YPYPYPYPYPYP ...

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Drug Design: PowerPoint PPT Presentation

Drug Design: - KJM5230-H04. Drug Design: Functional groups / Pharmacological Activity ... pH duodenum ca. 4. pH urine ca. 6. Identification of acidic / basic functional groups ...

KJM5230-H04. Drug Design: Functional groups / Pharmacological Activity ... pH duodenum ca. 4. pH urine ca. 6. Identification of acidic / basic functional groups ...

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Protein Structure Prediction PowerPoint PPT Presentation

Protein Structure Prediction - Consider PSP as performing a search through the configuration space of the given ... This is needed as trying to solve PSP is too complex for real proteins ...

Consider PSP as performing a search through the configuration space of the given ... This is needed as trying to solve PSP is too complex for real proteins ...

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Basic Organic Chemistry I PowerPoint PPT Presentation

Basic Organic Chemistry I - Review of Carbon Atom

Review of Carbon Atom

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HHMI meeting, FOLDING PowerPoint PPT Presentation

HHMI meeting, FOLDING - Title: HHMI meeting, FOLDING Author: AF Last modified by: Finkelstein Created Date: 6/6/2002 6:51:05 PM Document presentation format: Company

Title: HHMI meeting, FOLDING Author: AF Last modified by: Finkelstein Created Date: 6/6/2002 6:51:05 PM Document presentation format: Company

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Assignment 2: Introduction to the Insight II Modeling Package and the PDB File Structure and Retriev PowerPoint PPT Presentation

Assignment 2: Introduction to the Insight II Modeling Package and the PDB File Structure and Retriev - Protein/Nu-cleic Acid Complexes. Proteins, Peptides, Viruses. Molecular Type --Feb 5, 2002 ... Assignment 3: Construction and Analysis of the Pentapeptide Met ...

Protein/Nu-cleic Acid Complexes. Proteins, Peptides, Viruses. Molecular Type --Feb 5, 2002 ... Assignment 3: Construction and Analysis of the Pentapeptide Met ...

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Protein Secondary Structure II PowerPoint PPT Presentation

Protein Secondary Structure II - N = the number of repeating units per turn ... Atom (1) -O- hydrogen bonds to the 7th atom in the chain with an N = 2.2 (2.2 residues per turn) ...

N = the number of repeating units per turn ... Atom (1) -O- hydrogen bonds to the 7th atom in the chain with an N = 2.2 (2.2 residues per turn) ...

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The Anatomy and Taxonomy of Protein Structure PowerPoint PPT Presentation

The Anatomy and Taxonomy of Protein Structure - yellow and blue delineate sterically allowed conformations ... (Kabsch & Sander, 1983) and STRIDE (Frishman & Argos, 1995) are two of the more ...

yellow and blue delineate sterically allowed conformations ... (Kabsch & Sander, 1983) and STRIDE (Frishman & Argos, 1995) are two of the more ...

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Computational Protein Design: A problem in combinatorial optimization PowerPoint PPT Presentation

Computational Protein Design: A problem in combinatorial optimization - There are 20 different amino acids that can be part of the chain. ... Bond, angle, dihedral. i , j are positions in sequence. Ri is rotamer choice at position i ...

There are 20 different amino acids that can be part of the chain. ... Bond, angle, dihedral. i , j are positions in sequence. Ri is rotamer choice at position i ...

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Protein Design PowerPoint PPT Presentation

Protein Design - Title: CS Biology Author: latombe Last modified by: Charles Created Date: 2/6/2002 10:25:02 PM Document presentation format: On-screen Show Company

Title: CS Biology Author: latombe Last modified by: Charles Created Date: 2/6/2002 10:25:02 PM Document presentation format: On-screen Show Company

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Protein structure prediction. - Title: Protein folding. Anfinsen s experiments. Author: panch Last modified by: Anna Created Date: 10/8/2004 7:14:18 PM Document presentation format

Title: Protein folding. Anfinsen s experiments. Author: panch Last modified by: Anna Created Date: 10/8/2004 7:14:18 PM Document presentation format

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8. Protein Docking - 8. Protein Docking *

8. Protein Docking *

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Goals for Today PowerPoint PPT Presentation

Goals for Today - Goals for Today Introduce automated refinement and validation. Evaluate Rwork and Rfree for your ProK model. Refine ProK (automatic) Validate ProK (web server)

Goals for Today Introduce automated refinement and validation. Evaluate Rwork and Rfree for your ProK model. Refine ProK (automatic) Validate ProK (web server)

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Homework grades PowerPoint PPT Presentation

Homework grades - 3. Insertions and deletions. insertion. AHYATPTTT. AH---TPSS. deletion. Occur mostly between secondary structures, in the loop regions. ...

3. Insertions and deletions. insertion. AHYATPTTT. AH---TPSS. deletion. Occur mostly between secondary structures, in the loop regions. ...

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Electrochemical Approaches to Organic Synthesis PowerPoint PPT Presentation

Electrochemical Approaches to Organic Synthesis - Title: Slide 1 Last modified by: Eugene E Kwan Created Date: 8/15/2002 9:50:45 PM Document presentation format: On-screen Show Company: McMaster University

Title: Slide 1 Last modified by: Eugene E Kwan Created Date: 8/15/2002 9:50:45 PM Document presentation format: On-screen Show Company: McMaster University

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HHMI meeting, FOLDING - ... P P ' ' ' ' P F ' P ... nn pFasF fpa p F pdtFFtddTTFeffTt s d d e n n ...

... P P ' ' ' ' P F ' P ... nn pFasF fpa p F pdtFFtddTTFeffTt s d d e n n ...

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Structural Features Forces and energetics of binding andor deformation PowerPoint PPT Presentation

Structural Features Forces and energetics of binding andor deformation - Molecular Strain (DNA) Enthalpic-entropic compensation: DNA binding events with similar affinities ... Sequence-dependent energies of DNA deformation: ...

Molecular Strain (DNA) Enthalpic-entropic compensation: DNA binding events with similar affinities ... Sequence-dependent energies of DNA deformation: ...

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Two parts to successful model building - Two parts to successful model building

Two parts to successful model building

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Packing, Cavities PowerPoint PPT Presentation

Packing, Cavities - use Fourier transform to evaluate shape correlation function. correlation function includes shape and electrostatic complementarity of surfaces ...

use Fourier transform to evaluate shape correlation function. correlation function includes shape and electrostatic complementarity of surfaces ...

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Tertiary Structure Prediction Methods PowerPoint PPT Presentation

Tertiary Structure Prediction Methods - Title: Homology Modeling: principles, tools and techniques Author: supa Last modified by: Muhammed Sayed Created Date: 6/15/2002 7:21:30 AM Document presentation format

Title: Homology Modeling: principles, tools and techniques Author: supa Last modified by: Muhammed Sayed Created Date: 6/15/2002 7:21:30 AM Document presentation format

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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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Comparative Protein Modeling PowerPoint PPT Presentation

Comparative Protein Modeling - Title: No Slide Title Author: Medical Illustration Unit Last modified by: McNair1 Created Date: 10/24/1997 5:44:18 AM Document presentation format

Title: No Slide Title Author: Medical Illustration Unit Last modified by: McNair1 Created Date: 10/24/1997 5:44:18 AM Document presentation format

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Automated Refinement PowerPoint PPT Presentation

Automated Refinement - Estereochemistry comprises empirical information about chemical interactions ... CHIRALITY of a-carbons. PLANARITY of peptide bonds and aromatic side chains ...

Estereochemistry comprises empirical information about chemical interactions ... CHIRALITY of a-carbons. PLANARITY of peptide bonds and aromatic side chains ...

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Protein structure prediction. - Sometimes a few SSEs may be missing. Fold classification: structural similarity between folds is searched using ... Domains defined with SCOP and CATH ...

Sometimes a few SSEs may be missing. Fold classification: structural similarity between folds is searched using ... Domains defined with SCOP and CATH ...

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Current Status and Future Directions for TEXTAL PowerPoint PPT Presentation

Current Status and Future Directions for TEXTAL - targeting 'medium-res' maps (2.5-3.5A) builds 80-90% of models in medium-quality maps ... Vestibular cues reinforce stereo cues ...

targeting 'medium-res' maps (2.5-3.5A) builds 80-90% of models in medium-quality maps ... Vestibular cues reinforce stereo cues ...

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Structural Bioinformatics PowerPoint PPT Presentation

Structural Bioinformatics - Structural Bioinformatics. What is it ? What can it do for us ? Genomics ... Structural Bioinformatics. What does it do? If there is an experimental structure ...

Structural Bioinformatics. What is it ? What can it do for us ? Genomics ... Structural Bioinformatics. What does it do? If there is an experimental structure ...

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Rapid Protein Side-Chain Packing via Tree Decomposition PowerPoint PPT Presentation

Rapid Protein Side-Chain Packing via Tree Decomposition - Ab initio folding. Homology modeling. Protein threading. Stage 2: Loop Modeling ... ab. ac. clk. c. f. fgh. ij. remove dem. Side-Chain Packing Algorithm ...

Ab initio folding. Homology modeling. Protein threading. Stage 2: Loop Modeling ... ab. ac. clk. c. f. fgh. ij. remove dem. Side-Chain Packing Algorithm ...

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Prediction of pKa shifts in proteins using a discrete rotamer search and the Rosetta energy function PowerPoint PPT Presentation

Prediction of pKa shifts in proteins using a discrete rotamer search and the Rosetta energy function - Prediction of pKa shifts in proteins using a discrete rotamer search and the Rosetta energy function Ryan M Harrison, Jeffrey J Gray Baltimore Polytechnic Institute

Prediction of pKa shifts in proteins using a discrete rotamer search and the Rosetta energy function Ryan M Harrison, Jeffrey J Gray Baltimore Polytechnic Institute

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Homology Modelling - CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS TECHNICAL UNIVERSITY ... techniques to reduce time (from months to days) and cost (from $100.000 to $20.000/structure) ...

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS TECHNICAL UNIVERSITY ... techniques to reduce time (from months to days) and cost (from $100.000 to $20.000/structure) ...

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Efficient Energy Computation for Monte Carlo Simulation of Proteins PowerPoint PPT Presentation

Efficient Energy Computation for Monte Carlo Simulation of Proteins - Only few DOFs are changed at each step. Large sub-chains remain rigid between steps ... efficiency of MCS by reducing average time to accept/reject a new conformation ...

Only few DOFs are changed at each step. Large sub-chains remain rigid between steps ... efficiency of MCS by reducing average time to accept/reject a new conformation ...

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Folding - Anfinsen (1950's) showed reversibility of denaturation with urea ... hydrophobicity? presence of a clearly-defined (deep) energy minimum. ends. can't move ...

Anfinsen (1950's) showed reversibility of denaturation with urea ... hydrophobicity? presence of a clearly-defined (deep) energy minimum. ends. can't move ...

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Cecilia Clementi PowerPoint PPT Presentation

Cecilia Clementi - Prediction of protein functional states by multi-resolution protein modeling Cecilia Clementi Department of Chemistry Rice University Houston, Texas

Prediction of protein functional states by multi-resolution protein modeling Cecilia Clementi Department of Chemistry Rice University Houston, Texas

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Organic Chemistry - Organic Chemistry

Organic Chemistry

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Computational Structure-Based Redesign of Enzyme Activity PowerPoint PPT Presentation

Computational Structure-Based Redesign of Enzyme Activity - Computational Structure-Based Redesign of Enzyme Activity. Cheng-Yu Chen, Ivelin ... ROSETTA (RosettaDesign, ...) 1) Energy Function. 2) Conformational Sampling ...

Computational Structure-Based Redesign of Enzyme Activity. Cheng-Yu Chen, Ivelin ... ROSETTA (RosettaDesign, ...) 1) Energy Function. 2) Conformational Sampling ...

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Structure Visualization PowerPoint PPT Presentation

Structure Visualization - http://biochemistry.utoronto.ca/steipe/bioinformatics. Work through the Rasmol tutorial ! ... structure alignment and analysis of sequence alignments. ...

http://biochemistry.utoronto.ca/steipe/bioinformatics. Work through the Rasmol tutorial ! ... structure alignment and analysis of sequence alignments. ...

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Homology Modeling - pre-processing, singles, pairs. Desmet, Mayo. reduction in ... de-couple interaction graph into bi-connected components representing local dependencies ...

pre-processing, singles, pairs. Desmet, Mayo. reduction in ... de-couple interaction graph into bi-connected components representing local dependencies ...

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Putting biology to work for you: In vitro (directed) evolution and other techniques PowerPoint PPT Presentation

Putting biology to work for you: In vitro (directed) evolution and other techniques - ... antibody-like properties Vitamin b12-binding RNA aptamer Slide 10 Let the immune system make enzymes for you Wedemayer et al. (1997) Science 276, 1665-1669.

... antibody-like properties Vitamin b12-binding RNA aptamer Slide 10 Let the immune system make enzymes for you Wedemayer et al. (1997) Science 276, 1665-1669.

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Validation of NMRderived structures PowerPoint PPT Presentation

Validation of NMRderived structures - Bond lengths, bond angles, chirality, omega angles, side chain planarity. Overall quality: ... Distorted C -chirality. D-amino acid. Chris Spronk CMBI 2003 ...

Bond lengths, bond angles, chirality, omega angles, side chain planarity. Overall quality: ... Distorted C -chirality. D-amino acid. Chris Spronk CMBI 2003 ...

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Homology Modeling: Principles, tools and techniques PowerPoint PPT Presentation

Homology Modeling: Principles, tools and techniques - ... and include the distance, angle and dihedral values ... Stereochemical bond, angle, dihedral, improper. Homology mainchain and sidechain dihedrals ...

... and include the distance, angle and dihedral values ... Stereochemical bond, angle, dihedral, improper. Homology mainchain and sidechain dihedrals ...

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Automated phase improvement and model building with Parrot and Buccaneer PowerPoint PPT Presentation

Automated phase improvement and model building with Parrot and Buccaneer - Automated phase improvement and model building with Parrot and Buccaneer Kevin Cowtan cowtan@ysbl.york.ac.uk X-ray structure solution pipeline... Density modification ...

Automated phase improvement and model building with Parrot and Buccaneer Kevin Cowtan cowtan@ysbl.york.ac.uk X-ray structure solution pipeline... Density modification ...

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Lab 9.3a: Homology Modeling PowerPoint PPT Presentation

Lab 9.3a: Homology Modeling - Sequence alignment is the single most important step in homology modeling. ... LIG. Complete: Add ligands, substrates etc. to model. Analyse: Interpret and conclude ...

Sequence alignment is the single most important step in homology modeling. ... LIG. Complete: Add ligands, substrates etc. to model. Analyse: Interpret and conclude ...

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Total Synthesis of (-)-Balanol A potent Protein Kinase C inhibitor and Analogues - Total Synthesis of (-)-Balanol A potent Protein Kinase C inhibitor and Analogues

Total Synthesis of (-)-Balanol A potent Protein Kinase C inhibitor and Analogues

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Modeling conformational changes during docking PowerPoint PPT Presentation

Modeling conformational changes during docking - Modeling conformational changes during docking Martin Zacharias Physik-Department T38 Technische Universit t M nchen ALGORITHMS IN STRUCTURAL BIOINFORMATICS ...

Modeling conformational changes during docking Martin Zacharias Physik-Department T38 Technische Universit t M nchen ALGORITHMS IN STRUCTURAL BIOINFORMATICS ...

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Protein Structural Prediction PowerPoint PPT Presentation

Protein Structural Prediction - Protein Structural Prediction. Performance of Structure Prediction Methods ... A -hairpin connected with a crossover to a third -strand ...

Protein Structural Prediction. Performance of Structure Prediction Methods ... A -hairpin connected with a crossover to a third -strand ...

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Predictions of the Docking of an Engineered Antibody to Anthrax Toxin - Predictions of the Docking of an Engineered Antibody to Anthrax Toxin

Predictions of the Docking of an Engineered Antibody to Anthrax Toxin

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Supervisor: Professor Michel DROZ University of Geneva Department of Theoretical Physics PowerPoint PPT Presentation

Supervisor: Professor Michel DROZ University of Geneva Department of Theoretical Physics - The Biological Physics of Protein Folding: the Random Energy Model and ... Including hydrophobicity: -the 21th species is the water -in the 'empty' sites ...

The Biological Physics of Protein Folding: the Random Energy Model and ... Including hydrophobicity: -the 21th species is the water -in the 'empty' sites ...

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The third level of protein conformation is known as tertiary structure - The third level of protein conformation is known as tertiary structure

The third level of protein conformation is known as tertiary structure

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Performance of RosettaDock in CAPRI Rounds 35 PowerPoint PPT Presentation

Performance of RosettaDock in CAPRI Rounds 35 - Performance of RosettaDock in CAPRI Rounds 3-5 ... Ovine prion fab. 19. 1.93. 6.11. 0.42. 5. 196. U-H. Cohesin-dockerin. 11. 0.51. 0.99. 0.87. 1 ...

Performance of RosettaDock in CAPRI Rounds 3-5 ... Ovine prion fab. 19. 1.93. 6.11. 0.42. 5. 196. U-H. Cohesin-dockerin. 11. 0.51. 0.99. 0.87. 1 ...

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Time scales and molecular motions PowerPoint PPT Presentation

Time scales and molecular motions - Time scales and molecular motions. Atomic fluctuations, vibrations. ... 13C Chemical Shift Anisotropy. z. y. x. O. C. O. C. O. C. Many orientations in xy plane ...

Time scales and molecular motions. Atomic fluctuations, vibrations. ... 13C Chemical Shift Anisotropy. z. y. x. O. C. O. C. O. C. Many orientations in xy plane ...

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Rotamers PowerPoint PPT Presentations