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NMR of Proteins Couplings and dihedrals PowerPoint PPT Presentation
NMR of Proteins Couplings and dihedrals - NMR of Proteins - Couplings and dihedrals. Last time we saw how we use NMR to obtain some of the ... structural parameters required to determine 3D structures ...
NMR of Proteins - Couplings and dihedrals. Last time we saw how we use NMR to obtain some of the ... structural parameters required to determine 3D structures ...
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NMR Steered Sampling Conformation Sampling via MC Rotation of Dihedrals Selected from NMR Experiment PowerPoint PPT Presentation
NMR Steered Sampling Conformation Sampling via MC Rotation of Dihedrals Selected from NMR Experiment - Perform steered sampling to rapidly identify clusters. Base docking ensemble on these experimentally supported clusters. Our Contribution ...
Perform steered sampling to rapidly identify clusters. Base docking ensemble on these experimentally supported clusters. Our Contribution ...
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Kinetics of liquid crystal phase transitions: PowerPoint PPT Presentation
Kinetics of liquid crystal phase transitions: - Conjugation. Dihedrals (torsion) VR. Bij VA. Carbon potential ... Conjugation. Dihedrals (torsion) In depth: angular interactions. G. Coordination three or more ...
Conjugation. Dihedrals (torsion) VR. Bij VA. Carbon potential ... Conjugation. Dihedrals (torsion) In depth: angular interactions. G. Coordination three or more ...
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AUTODOCK An Automated Docking Software for Predicting Optimal ProteinLigand Interaction PowerPoint PPT Presentation
AUTODOCK An Automated Docking Software for Predicting Optimal ProteinLigand Interaction - Quaternion reduction factor = 1. Torsional reduction factor = 1 # rotatable bonds = 12 ... Initial quaternion = Random. Initial dihedrals = Random. Translation ...
Quaternion reduction factor = 1. Torsional reduction factor = 1 # rotatable bonds = 12 ... Initial quaternion = Random. Initial dihedrals = Random. Translation ...
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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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Computational issues in Carbon nanotube simulation PowerPoint PPT Presentation
Computational issues in Carbon nanotube simulation - ... of each atom. Force computations. Bond angles. Pair interactions ... For each bond, compute forces due to that bond, angles, and dihedrals. Finer grained ...
... of each atom. Force computations. Bond angles. Pair interactions ... For each bond, compute forces due to that bond, angles, and dihedrals. Finer grained ...
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WRIGHT STUFF PowerPoint PPT Presentation
WRIGHT STUFF - Title: WRIGHT STUFF Author: dbraunstein Last modified by: dbraunstein Created Date: 2/2/2006 6:07:54 PM Document presentation format: On-screen Show (4:3)
Title: WRIGHT STUFF Author: dbraunstein Last modified by: dbraunstein Created Date: 2/2/2006 6:07:54 PM Document presentation format: On-screen Show (4:3)
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Questions PowerPoint PPT Presentation
Questions - Questions Blue should have been covered in lecture. If you still have questions. Please,Ask! 1) Are the values of r0/theta0 approximately what is listed in the book ...
Questions Blue should have been covered in lecture. If you still have questions. Please,Ask! 1) Are the values of r0/theta0 approximately what is listed in the book ...
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WRIGHT STUFF PowerPoint PPT Presentation
WRIGHT STUFF - wright stuff agenda introduction aircraft terminology theory of flight glider details hints extra--starting plans dave braunstein academic coordinator mesa csulb 35 ...
wright stuff agenda introduction aircraft terminology theory of flight glider details hints extra--starting plans dave braunstein academic coordinator mesa csulb 35 ...
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Applying Target Decomposition Algorithms on the Detection of Man Made Targets Using Polarimetric SAR PowerPoint PPT Presentation
Applying Target Decomposition Algorithms on the Detection of Man Made Targets Using Polarimetric SAR - Test this methodology with a more diverse set of target ... Erasing 1 and 2-pixel detections. Morphological processing. 14. Experiments: data sets used (1) ...
Test this methodology with a more diverse set of target ... Erasing 1 and 2-pixel detections. Morphological processing. 14. Experiments: data sets used (1) ...
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Molecular Dynamics Method 2 PowerPoint PPT Presentation
Molecular Dynamics Method 2 - Example: Gramicidin A Peptide. D-Val and D-Leu residues ... Example: Solvating Gramicidin. Begin with a block of equilibrated water. ...
Example: Gramicidin A Peptide. D-Val and D-Leu residues ... Example: Solvating Gramicidin. Begin with a block of equilibrated water. ...
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Co-processors for speeding up drug design algorithms PowerPoint PPT Presentation
Co-processors for speeding up drug design algorithms - To design FPGA based hardware accelerators for speeding up the energy minimization process. ... Hardware Design. Performance Analysis. Overall Control Flow ...
To design FPGA based hardware accelerators for speeding up the energy minimization process. ... Hardware Design. Performance Analysis. Overall Control Flow ...
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Forward and inverse kinematics in RNA backbone conformations PowerPoint PPT Presentation
Forward and inverse kinematics in RNA backbone conformations - Forward and inverse kinematics in RNA backbone ... 99% backbone steric clashes are within suites. 42 Conformations. A-form RNA accounts for 75% data ...
Forward and inverse kinematics in RNA backbone ... 99% backbone steric clashes are within suites. 42 Conformations. A-form RNA accounts for 75% data ...
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High%20Throughput%20Computing%20and%20Protein%20Structure PowerPoint PPT Presentation
High%20Throughput%20Computing%20and%20Protein%20Structure - Finding the secondary structure of a protein is a step towards ... Can we use a program like Trepan to get some definite rules about secondary structure. ...
Finding the secondary structure of a protein is a step towards ... Can we use a program like Trepan to get some definite rules about secondary structure. ...
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Coprocessors for speeding up drug design algorithms PowerPoint PPT Presentation
Coprocessors for speeding up drug design algorithms - To design FPGA based hardware accelerators for speeding up the energy minimization process. ... Multiple threads operating on the Non-bonded list together. ...
To design FPGA based hardware accelerators for speeding up the energy minimization process. ... Multiple threads operating on the Non-bonded list together. ...
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Geometric Methods for Improving RNA Structure PowerPoint PPT Presentation
Geometric Methods for Improving RNA Structure - Steric clashes (collisions) occur when non-bonded atoms are too close. d. Ribosome ... Use forward kinematics to remove steric clashes in a dinucleotide ...
Steric clashes (collisions) occur when non-bonded atoms are too close. d. Ribosome ... Use forward kinematics to remove steric clashes in a dinucleotide ...
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Unified Rigidity and Kinematic Analysis of Proteins PowerPoint PPT Presentation
Unified Rigidity and Kinematic Analysis of Proteins - Consider a first-order Taylor Series expansion of the constraint equations about ... Can be optimised to reduce steric clashes and/or take account of dihedral angles ...
Consider a first-order Taylor Series expansion of the constraint equations about ... Can be optimised to reduce steric clashes and/or take account of dihedral angles ...
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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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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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Molecular Dynamics Simulations of CinchonidineModified Platinum in Ethanol PowerPoint PPT Presentation
Molecular Dynamics Simulations of CinchonidineModified Platinum in Ethanol - Molecular Dynamics Simulations of CinchonidineModified Platinum in Ethanol
Molecular Dynamics Simulations of CinchonidineModified Platinum in Ethanol
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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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Energetics of Secondary Structural Elements PowerPoint PPT Presentation
Energetics of Secondary Structural Elements - A type of attractive intermolecular force that exists ... EIMPR: describes the improper angle energies (planarity and chirality)? Nonbonded Energy Terms: ...
A type of attractive intermolecular force that exists ... EIMPR: describes the improper angle energies (planarity and chirality)? Nonbonded Energy Terms: ...
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The 3D structure of RNA backbone Xueyi Wang and Jack Snoeyink Department of Computer Science, UNCCha PowerPoint PPT Presentation
The 3D structure of RNA backbone Xueyi Wang and Jack Snoeyink Department of Computer Science, UNCCha - Department of Computer Science, UNC-Chapel Hill ... d-e-? dihedral plot. a- -? dihedral plot. d-e-? clash plot. measurement plot ...
Department of Computer Science, UNC-Chapel Hill ... d-e-? dihedral plot. a- -? dihedral plot. d-e-? clash plot. measurement plot ...
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Exact Analytical Formulation PowerPoint PPT Presentation
Exact Analytical Formulation - Small Peptide Ring Efficient Conformational Search ... (quaternion notation) Altering an internal dihedral leads to a 'nearby' loop closure problem. ...
Small Peptide Ring Efficient Conformational Search ... (quaternion notation) Altering an internal dihedral leads to a 'nearby' loop closure problem. ...
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Improved Hybrid Monte Carlo method for conformational sampling PowerPoint PPT Presentation
Improved Hybrid Monte Carlo method for conformational sampling - Improved Hybrid Monte Carlo method for conformational sampling Jes s A. Izaguirre with Scott Hampton Department of Computer Science and Engineering
Improved Hybrid Monte Carlo method for conformational sampling Jes s A. Izaguirre with Scott Hampton Department of Computer Science and Engineering
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An Optimization Approach to Protein Structure Prediction PowerPoint PPT Presentation
An Optimization Approach to Protein Structure Prediction - Robert Schnabel. Brett Bader. Lianjun Jiang. University of Colorado ... Ruckzinski, Kooperberg, Bonneau, and Baker. Proteins 48, 2002. Parallel Organization ...
Robert Schnabel. Brett Bader. Lianjun Jiang. University of Colorado ... Ruckzinski, Kooperberg, Bonneau, and Baker. Proteins 48, 2002. Parallel Organization ...
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Classical Force Fields PowerPoint PPT Presentation
Classical Force Fields - membrane, protein insertion kinetics. mechanism, protein ... AICAR IMPG. Histidine. Biosynthesis. Purine Biosynthesis. Imidazole Glycerol Phosphate Synthase: ...
membrane, protein insertion kinetics. mechanism, protein ... AICAR IMPG. Histidine. Biosynthesis. Purine Biosynthesis. Imidazole Glycerol Phosphate Synthase: ...
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Introduction into Molecular Dynamics Ralf Schneider, Abha Rai, Amit Rai Sharma PowerPoint PPT Presentation
Introduction into Molecular Dynamics Ralf Schneider, Abha Rai, Amit Rai Sharma - Outline: 1. Basics 2. Potentials 3. History 4. Numerics 5. Analysis of MD runs (6. Physics extensions= 7. Numerical extensions 8. Summary Introduction into Molecular ...
Outline: 1. Basics 2. Potentials 3. History 4. Numerics 5. Analysis of MD runs (6. Physics extensions= 7. Numerical extensions 8. Summary Introduction into Molecular ...
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(Bio)-applications of high-field NMR PowerPoint PPT Presentation
(Bio)-applications of high-field NMR - (Bio)-applications of high-field NMR Aims To give an overview of the capability of NMR to answer biological questions To make aware of limitations To give a basic ...
(Bio)-applications of high-field NMR Aims To give an overview of the capability of NMR to answer biological questions To make aware of limitations To give a basic ...
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Molecular dynamics and applications to amyloidogenic sequences PowerPoint PPT Presentation
Molecular dynamics and applications to amyloidogenic sequences - Molecular dynamics: goals, applications and basic principles: Newton's equations of motion. ... Study the time development of the system. ...
Molecular dynamics: goals, applications and basic principles: Newton's equations of motion. ... Study the time development of the system. ...
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Molecular Modeling Techniques are a Critical Component of Determining a Protein Structure by NMR: PowerPoint PPT Presentation
Molecular Modeling Techniques are a Critical Component of Determining a Protein Structure by NMR: - Molecular Modeling Techniques are a Critical Component of Determining a Protein Structure by NMR: ... The molecular potential U depends on two types of variables: ...
Molecular Modeling Techniques are a Critical Component of Determining a Protein Structure by NMR: ... The molecular potential U depends on two types of variables: ...
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What have you learned in the previous lectures PowerPoint PPT Presentation
What have you learned in the previous lectures - Most proteins interact at least transiently with other proteins, but it is clear ... research. ... higher temperatures salt bridges make more of a contribution ...
Most proteins interact at least transiently with other proteins, but it is clear ... research. ... higher temperatures salt bridges make more of a contribution ...
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Seminar 1' Protein Biophysics Notes M'Buck 32007 PowerPoint PPT Presentation
Seminar 1' Protein Biophysics Notes M'Buck 32007 - Seminar 1. Protein Biophysics Notes M.Buck 3/20/07 ... RMSD = [ 1/N Sk=1 to N (rik rjk)2] (unit in distance, i.e. Angstrom) ...
Seminar 1. Protein Biophysics Notes M.Buck 3/20/07 ... RMSD = [ 1/N Sk=1 to N (rik rjk)2] (unit in distance, i.e. Angstrom) ...
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Computational issues in nanotechnology and stochastic computing PowerPoint PPT Presentation
Computational issues in nanotechnology and stochastic computing - Computational issues in nanotechnology and stochastic computing ... Applications needing large amounts of computational power. Nanotechnology. Pharmaceuticals ...
Computational issues in nanotechnology and stochastic computing ... Applications needing large amounts of computational power. Nanotechnology. Pharmaceuticals ...
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Introduction into Molecular Dynamics Ralf Schneider, Abha Rai, Amit Rai Sharma PowerPoint PPT Presentation
Introduction into Molecular Dynamics Ralf Schneider, Abha Rai, Amit Rai Sharma - Solve Newton's equation for a molecular system: ... macroscopic numbers of atoms or molecules (of the order of 1023, Avogadro's ...
Solve Newton's equation for a molecular system: ... macroscopic numbers of atoms or molecules (of the order of 1023, Avogadro's ...
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Hydrophobic Residue Patterning in Strands and Implications for Sheet Nucleation PowerPoint PPT Presentation
Hydrophobic Residue Patterning in Strands and Implications for Sheet Nucleation - ROSETTA. Pioneered by Baker Group (U. of Washington) Fragment ... ROSETTA. Pre-build fragment library. 3-mers and 9-mers. 200 structural possibilities for each ...
ROSETTA. Pioneered by Baker Group (U. of Washington) Fragment ... ROSETTA. Pre-build fragment library. 3-mers and 9-mers. 200 structural possibilities for each ...
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Introduction into Molecular Dynamics Ralf Schneider, Abha Rai, Amit Rai Sharma PowerPoint PPT Presentation
Introduction into Molecular Dynamics Ralf Schneider, Abha Rai, Amit Rai Sharma - Outline: 1. Basics 2. Potentials 3. History 4. Numerics 5. Analysis of MD runs (6. Physics extensions= 7. Numerical extensions 8. Summary Introduction into Molecular ...
Outline: 1. Basics 2. Potentials 3. History 4. Numerics 5. Analysis of MD runs (6. Physics extensions= 7. Numerical extensions 8. Summary Introduction into Molecular ...
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NIH Resource for Biomolecular Modeling and Bioinformatics PowerPoint PPT Presentation
NIH Resource for Biomolecular Modeling and Bioinformatics - The Flying Ice Cube. a molecular dynamics horror story ... a molecular dynamics fairy tale ... a molecular dynamics fairy tale. Steering forces are needed to ...
The Flying Ice Cube. a molecular dynamics horror story ... a molecular dynamics fairy tale ... a molecular dynamics fairy tale. Steering forces are needed to ...
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Molecular Modeling Techniques are a Critical Component of Determining a Protein Structure by NMR: PowerPoint PPT Presentation
Molecular Modeling Techniques are a Critical Component of Determining a Protein Structure by NMR: - Molecular Modeling Techniques are a Critical Component of Determining a Protein ... determines magnitude of function (force constant) typically 20-50 kcal/mole ...
Molecular Modeling Techniques are a Critical Component of Determining a Protein ... determines magnitude of function (force constant) typically 20-50 kcal/mole ...
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V5: Exploring energy landscapes for protein folding: by allatom MD simulations PowerPoint PPT Presentation
V5: Exploring energy landscapes for protein folding: by allatom MD simulations - Traditional procedures for the experimental determination of protein structures: ... data using a constant temperature Weighted Histogram Analysis Method (WHAM) ...
Traditional procedures for the experimental determination of protein structures: ... data using a constant temperature Weighted Histogram Analysis Method (WHAM) ...
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NMR Spectroscopy and Protein Structures PowerPoint PPT Presentation
NMR Spectroscopy and Protein Structures - NMR Spectroscopy and Protein Structures
NMR Spectroscopy and Protein Structures
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Lecture 9'2: Homology and Structural Similarity What to do when you have no structure ''' PowerPoint PPT Presentation
Lecture 9'2: Homology and Structural Similarity What to do when you have no structure ''' - RMSDopt = RMSDcoord(A, (B-Ts) x Rs) ... Dill KA & Chan HS (1997) From Levinthal to pathways to funnels. Nature Struct Biol 4:10-19 ...
RMSDopt = RMSDcoord(A, (B-Ts) x Rs) ... Dill KA & Chan HS (1997) From Levinthal to pathways to funnels. Nature Struct Biol 4:10-19 ...
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Protein NMR III Other types of structural data PowerPoint PPT Presentation
Protein NMR III Other types of structural data - Protein NMR III - Other types of structural data. In the last two classes we looked at how we ... The idea is that labile protons (NHs) that are protected from ...
Protein NMR III - Other types of structural data. In the last two classes we looked at how we ... The idea is that labile protons (NHs) that are protected from ...
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Descriptive Geometry PowerPoint PPT Presentation
Descriptive Geometry - This is ppt show for Descriptive Geometry. This is a subject that deals with orthographic projection of points, lines, planes as well as solids. The subject helps in developing the concept of orthographic projection.
This is ppt show for Descriptive Geometry. This is a subject that deals with orthographic projection of points, lines, planes as well as solids. The subject helps in developing the concept of orthographic projection.
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Activation of the Cannabinoid CB1 Receptor May Involve a W6.48F3.36 Rotamer Toggle Switch PowerPoint PPT Presentation
Activation of the Cannabinoid CB1 Receptor May Involve a W6.48F3.36 Rotamer Toggle Switch - Analysis:The proline kink, wobble and face shift angles for each set of 100 ... The L6.44F mutant has a reduced proline kink bend angle relative to WT (table 4) ...
Analysis:The proline kink, wobble and face shift angles for each set of 100 ... The L6.44F mutant has a reduced proline kink bend angle relative to WT (table 4) ...
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1. dia PowerPoint PPT Presentation
1. dia - chapter 3 structure and properties of molecules
chapter 3 structure and properties of molecules
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Protein Chemistry Basics PowerPoint PPT Presentation
Protein Chemistry Basics - Protein Chemistry Basics Protein function Protein structure Primary Amino acids Linkage Protein conformation framework Dihedral angles Ramachandran plots
Protein Chemistry Basics Protein function Protein structure Primary Amino acids Linkage Protein conformation framework Dihedral angles Ramachandran plots
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NMR Spectroscopy PowerPoint PPT Presentation
NMR Spectroscopy - Anisotropy. Ring current. Electric field effect. Intermolecular interaction ... anisotropy ... of the chemical shift anisotropy - symmetry at the nuclear site ...
Anisotropy. Ring current. Electric field effect. Intermolecular interaction ... anisotropy ... of the chemical shift anisotropy - symmetry at the nuclear site ...
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Website: http://www.rubber-power.com PowerPoint PPT Presentation
Website: http://www.rubber-power.com - Website: http://www.rubber-power.com Article by Bill Kuhl http://www.scienceguy.org Special Thanks to Darcy Whyte for all his help! Mods Several people have sent ...
Website: http://www.rubber-power.com Article by Bill Kuhl http://www.scienceguy.org Special Thanks to Darcy Whyte for all his help! Mods Several people have sent ...
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Dynameomics: Protein Mechanics, Folding and Unfolding through Large Scale All-Atom Molecular Dynamics Simulations PowerPoint PPT Presentation
Dynameomics: Protein Mechanics, Folding and Unfolding through Large Scale All-Atom Molecular Dynamics Simulations - Dynameomics: Protein Mechanics, Folding and Unfolding through Large Scale All-Atom Molecular Dynamics Simulations INCITE 6 David A. C. Beck Valerie Daggett Research Group
Dynameomics: Protein Mechanics, Folding and Unfolding through Large Scale All-Atom Molecular Dynamics Simulations INCITE 6 David A. C. Beck Valerie Daggett Research Group
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NMR (Nuclear Magnetic Resonance Spectroscopy) PowerPoint PPT Presentation
NMR (Nuclear Magnetic Resonance Spectroscopy) - Basic NMR Metric matrix method Variable target function method
Basic NMR Metric matrix method Variable target function method
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Stereochemistry PowerPoint PPT Presentation
Stereochemistry - Smita Asthana @ St.Ann's
Smita Asthana @ St.Ann's
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INCIDENCE GEOMETRIES PowerPoint PPT Presentation
INCIDENCE GEOMETRIES - Substructures, Symmetry and Duality. Haar Graphs and Cyclic Configurations. Algebraic Structures ... automorphisms we speak of dualities that map faces of rank ...
Substructures, Symmetry and Duality. Haar Graphs and Cyclic Configurations. Algebraic Structures ... automorphisms we speak of dualities that map faces of rank ...
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INCIDENCE GEOMETRIES PowerPoint PPT Presentation
INCIDENCE GEOMETRIES - Euclidean Plane, Affine Plane, Projective Plane ... (See Egon Shulte, ..., Tits systems) The 4-Dimensional Cube Q4. 0000. 1000. 0010. 0100 ...
Euclidean Plane, Affine Plane, Projective Plane ... (See Egon Shulte, ..., Tits systems) The 4-Dimensional Cube Q4. 0000. 1000. 0010. 0100 ...
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HHybrid Monte Carlo method for conformational sampling of proteins PowerPoint PPT Presentation
HHybrid Monte Carlo method for conformational sampling of proteins - HHybrid Monte Carlo method for conformational sampling of proteins Jes s A. Izaguirre with Scott Hampton Department of Computer Science and Engineering
HHybrid Monte Carlo method for conformational sampling of proteins Jes s A. Izaguirre with Scott Hampton Department of Computer Science and Engineering
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Compact Polarimetry Potentials PowerPoint PPT Presentation
Compact Polarimetry Potentials - Compact Polarimetry Potentials My-Linh Truong-Lo , Jet Propulsion Laboratory / California Institue of Technology Eric Pottier, IETR, UMR CNRS 6164
Compact Polarimetry Potentials My-Linh Truong-Lo , Jet Propulsion Laboratory / California Institue of Technology Eric Pottier, IETR, UMR CNRS 6164
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