Computational Molecular Modeling
|
|
- Florence Montgomery
- 5 years ago
- Views:
Transcription
1 Computational Molecular Modeling Lecture 1: Structure Models, Properties Chandrajit Bajaj
2 Today s Outline Intro to atoms, bonds, structure, biomolecules, Geometry of Proteins, Nucleic Acids, Ribosomes, Viruses Space Occupancy, Bonded, Non-Bonded Areas, Volumes, Derivatives Dynamic Maintenance and Bioinformatics
3 The Tree of Life! The World of the Cell, 1996) Eukaryotic cells Viruses? Ribosome Prokaryotic cell The problems of chemistry and biology can be greatly helped if our ability to see what we are doing, and to do things on an atomic level, is ultimately developed - a development which I think cannot be avoided Richard Feynman, 1959 CalTech
4 The Tree of Life! The World of the Cell, 1996) Eukaryotic cells Viruses? Ribosome Prokaryotic cell The problems of chemistry and biology can be greatly helped if our ability to see what we are doing, and to do things on an atomic level, is ultimately developed - a development which I think cannot be avoided Richard Feynman, 1959 CalTech
5
6 X-ray diffraction analysis for Atomic Resolution Structure Determination X-ray crystallography (diffraction) Atomic resolution Difficulties (experimental, computational) human deoxy-hemoglobin Protein Data Bank
7 Xray Crystallography- elucidating structure Ø Periodicity and Symmetry in a Crystal Ø Diffraction Pattern and Bragg s Law Ø Reciprocal Space and Fourier Transform Ø Phase Problem and Solutions Ø Fitting, Refinement, and Validation Crystal à Diffraction pattern à Electron density à Model
8 Molecular Structure of Hemoglobin secondary, tertiary, quaternary structure One myoglobin chain contains eight α-helices and no β -sheets. Nobel Prize
9 The PDB file ATOM 1 N GLU A ATOM 2 CA GLU A ATOM 3 C GLU A ATOM 4 O GLU A ATOM 5 CB GLU A ATOM 6 CG GLU A ATOM 7 CD GLU A ATOM 8 OE1 GLU A ATOM 9 OE2 GLU A ATOM 10 N ARG A ATOM 11 CA ARG A ATOM 12 C ARG A ATOM 13 O ARG A ATOM 14 CB ARG A ATOM 15 CG ARG A ATOM 16 CD ARG A ATOM 17 NE ARG A ATOM 18 CZ ARG A ATOM 19 NH1 ARG A ATOM 20 NH2 ARG A
10 PDB -> 2--> PQR Replace the temperature and occupancy columns with per-atom charge (Q) and radius (R) for a PDB file. Field Atom_num Atom_name Res_name Chain_ID Res_numr X Y Z temp occupy ATOM CB LYS L C ATOM CG LYS L C ATOM CD LYS L C Field Atom_num Atom_name Res_name Chain_ID Res_numr X Y Z Charge Radius ATOM CB LYS L C ATOM CG LYS L C ATOM CD LYS L C Two widely used approaches: PDB2PQR and Amber
11 What is the atomic charge? Atomic Charges Based on atomic electronegativity, optimized for a given Force Field. example: Gasteiger charges. Based on atomic electronegativity and the resulting electrical field. example: Charge Equilibrium charges (QEq). * Based on the electronic distribution calculated by QM. example: Mulliken charges. Based on the electrostatic potential near the molecule, calculated by a non-empirical method (or determined experimentally). examples: Chelp, ChelpG, RESP. Center for Computational Visualization Institute for Computational and Engineering Sciences Sep 2011
12
13
14
15 Proteins Amino acids contain an amide, a residue and a carboxyl group Proteins are polypeptide chains, made from amino acids combined via peptide bonds. H H N R Cα H C O OH N H R Cα H C O H N H Cα R O C
16 Amino Acids (I) Unlabeled atoms are either carbon or hydrogen. C alpha atoms are shaded. Double bonds and partially double bonds are shown in bold.
17 Amino Acids (II) Unlabeled atoms are either carbon or hydrogen. C alpha atoms are shaded. Double bonds and partially double bonds are shown in bold.
18 Protein Geometry: Backbone + SideChains
19 Figure Phil Bradley:
20
21
22
23 Figure Phil Bradley:
24 Figure Phil Bradley:
25 Figure Phil Bradley:
26 Figure Phil Bradley:
27
28 Figure Phil Bradley:
29 Figure Phil Bradley:
30 Figure Phil Bradley:
31 Figure Phil Bradley:
32 Figure Phil Bradley:
33 Figure Phil Bradley:
34 Figure Phil Bradley:
35 Figure Phil Bradley:
36 Figure Phil Bradley:
37 Figure Phil Bradley:
38 Figure Phil Bradley:
39 RNA:Ribo-Nucleic Acids α β P H5 O5 γ H4 C5 δ Torsion angles C4 H3 H5 C3 ε O3 ζ P Phosphoric acid Adenine, Guanine, Cytosine, Uracil. O4 C2 H2 χ C1 H2 Base C5 Nucleotide C4 Sugar C3 C1 C2 Phosphoric acid Can also specify ribose dihedral angles and puckering phase, amplitude Base C5 RNA polymer Nucleotide Base Sugar C1 C4 C3 C2
40 Bases
41 Figure Phil Bradley:
42 Molecular Models I Solvent molecule modeled as a probe sphere. Water: radius 1.4A Probe sphere SAS 1NT5 Molecule VDW SES/SCS SAS: solvent accessible : locus of probe center VDW: van der Waals: Union of spheres with VDW radii SES/SCS: solvent excluded/solvent contact --- Molecular surface
43 Power Diagram & Union of Balls (vdw) Union of disks (CPK) Laguerre Voronoi (Power) Diagram Regular Triangulation Skeletal Complex
44 Laguerre Geometry & Union of Balls H. Edelsbrunner. The union of balls and its dual shape. Disc. Comput. Geom., 13: , C. Bajaj, V. Pascucci, A. Shamir, R. Holt, A. Netravali Dynamic Maintenance and Visualization of Molecular Surfaces Discrete Applied Mathematics 127 (2003). Pages
45 Adaptive Grids & Union of Balls Legend Gridpoint: l VDW (red) l SAS (green) l OUT (unmarked) Gridcell: l Buried (brown) l VDWBoundary (light green) l SASBand (dark blue) l SASBoundary (light blue) l Out (white) l Gridpoint classes l Gridcell classes
46 Adap. Grids & Updating Union of Balls Add l l l l Gridpoints can be reclassified l SAS -> VDW, OUT -> SAS, OUT ->VDW Gridcell classification is also changed based on new classification of gridpoints The new atom is marked as exposed if its insertion resulted in marking a gridpoint as SAS Previously exposed atoms intersecting the new atom are marked buried if their SAS volume does not contain any gridpoint marked SAS l Add is O(1) under the assumption that the grid-spacing h = O(r s ) and r s = O(r max )
47 Adap. Grids & Updating Union of Balls Remove l l l Gridpoints can be reclassified l SAS -> OUT, VDW -> SAS, VDW ->OUT Gridcell classification is also changed based on new classification of gridpoints Previously buried atoms intersecting the removed atom can become exposed if their SAS volume now contain any gridpoint marked SAS l Removal is O(1) under the assumption that the grid-spacing h = O(r s ) and r s = O(r max )
48 Structural Properties _I
49 Structural Properties _II
50 Structural Properties _III We shall correct this critical problem in the next lecture on Smooth Structural Interfaces!
51 Challenge #2: Bimolecular Models in Solvent Computational Problems Smooth Interfaces Parameterization Area and Volume Derivatives Dynamic Updates Techniques nfft for fast summations Fast Dynamic Particle Maintenance Integrals, Quadrature Challenges Protein Flexibility Protein Folding, Rotamer Packing Spontaneous Assembly NEXT Aperiodic Quasi-crystals or Quasi-lattices
52 Some Useful Software Links Some useful Structure Links The molecular energetics and docking client /viewer TexMol and a user-manual The molecular viewer PyMOL and this tutorial The program MODELLER. Some useful Databases/Servers The PDB, the repository of experimentally determined protein structures. NCBI PSI-Blast. MUSCLE protein multiple sequence alignment server. PredictProtein protein sequence analysis web server: secondary structure prediction, coiled-coils, transmembrane helices, fold recognition,... PROSITE protein sequence patterns. SCOP structure classification database. matrix2png, a handy bioinformatics tool. Bioinfo MetaServer, consensus fold recognition server.
Protein structure (and biomolecular structure more generally) CS/CME/BioE/Biophys/BMI 279 Sept. 28 and Oct. 3, 2017 Ron Dror
Protein structure (and biomolecular structure more generally) CS/CME/BioE/Biophys/BMI 279 Sept. 28 and Oct. 3, 2017 Ron Dror Please interrupt if you have questions, and especially if you re confused! Assignment
More informationRanjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India. 1 st November, 2013
Hydration of protein-rna recognition sites Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India 1 st November, 2013 Central Dogma of life DNA
More informationFrom Amino Acids to Proteins - in 4 Easy Steps
From Amino Acids to Proteins - in 4 Easy Steps Although protein structure appears to be overwhelmingly complex, you can provide your students with a basic understanding of how proteins fold by focusing
More informationALL LECTURES IN SB Introduction
1. Introduction 2. Molecular Architecture I 3. Molecular Architecture II 4. Molecular Simulation I 5. Molecular Simulation II 6. Bioinformatics I 7. Bioinformatics II 8. Prediction I 9. Prediction II ALL
More informationProtein Structures. 11/19/2002 Lecture 24 1
Protein Structures 11/19/2002 Lecture 24 1 All 3 figures are cartoons of an amino acid residue. 11/19/2002 Lecture 24 2 Peptide bonds in chains of residues 11/19/2002 Lecture 24 3 Angles φ and ψ in the
More informationCh 3: Chemistry of Life. Chemistry Water Macromolecules Enzymes
Ch 3: Chemistry of Life Chemistry Water Macromolecules Enzymes Chemistry Atom = smallest unit of matter that cannot be broken down by chemical means Element = substances that have similar properties and
More informationIntroduction to Comparative Protein Modeling. Chapter 4 Part I
Introduction to Comparative Protein Modeling Chapter 4 Part I 1 Information on Proteins Each modeling study depends on the quality of the known experimental data. Basis of the model Search in the literature
More informationExamples of Protein Modeling. Protein Modeling. Primary Structure. Protein Structure Description. Protein Sequence Sources. Importing Sequences to MOE
Examples of Protein Modeling Protein Modeling Visualization Examination of an experimental structure to gain insight about a research question Dynamics To examine the dynamics of protein structures To
More informationProtein Dynamics. The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron.
Protein Dynamics The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron. Below is myoglobin hydrated with 350 water molecules. Only a small
More informationCOMP 598 Advanced Computational Biology Methods & Research. Introduction. Jérôme Waldispühl School of Computer Science McGill University
COMP 598 Advanced Computational Biology Methods & Research Introduction Jérôme Waldispühl School of Computer Science McGill University General informations (1) Office hours: by appointment Office: TR3018
More informationCAP 5510 Lecture 3 Protein Structures
CAP 5510 Lecture 3 Protein Structures Su-Shing Chen Bioinformatics CISE 8/19/2005 Su-Shing Chen, CISE 1 Protein Conformation 8/19/2005 Su-Shing Chen, CISE 2 Protein Conformational Structures Hydrophobicity
More informationBasics of protein structure
Today: 1. Projects a. Requirements: i. Critical review of one paper ii. At least one computational result b. Noon, Dec. 3 rd written report and oral presentation are due; submit via email to bphys101@fas.harvard.edu
More informationBiomolecules. Energetics in biology. Biomolecules inside the cell
Biomolecules Energetics in biology Biomolecules inside the cell Energetics in biology The production of energy, its storage, and its use are central to the economy of the cell. Energy may be defined as
More informationMolecular Modeling lecture 2
Molecular Modeling 2018 -- lecture 2 Topics 1. Secondary structure 3. Sequence similarity and homology 2. Secondary structure prediction 4. Where do protein structures come from? X-ray crystallography
More information1. (5) Draw a diagram of an isomeric molecule to demonstrate a structural, geometric, and an enantiomer organization.
Organic Chemistry Assignment Score. Name Sec.. Date. Working by yourself or in a group, answer the following questions about the Organic Chemistry material. This assignment is worth 35 points with the
More informationIntroduction to" Protein Structure
Introduction to" Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Learning Objectives Outline the basic levels of protein structure.
More informationUseful background reading
Overview of lecture * General comment on peptide bond * Discussion of backbone dihedral angles * Discussion of Ramachandran plots * Description of helix types. * Description of structures * NMR patterns
More informationProtein Data Bank Contents Guide: Atomic Coordinate Entry Format Description. Version Document Published by the wwpdb
Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description Version 3.30 Document Published by the wwpdb This format complies with the PDB Exchange Dictionary (PDBx) http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/index/index.html.
More informationHOMOLOGY MODELING. The sequence alignment and template structure are then used to produce a structural model of the target.
HOMOLOGY MODELING Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental
More informationProtein Bioinformatics Computer lab #1 Friday, April 11, 2008 Sean Prigge and Ingo Ruczinski
Protein Bioinformatics 260.655 Computer lab #1 Friday, April 11, 2008 Sean Prigge and Ingo Ruczinski Goals: Approx. Time [1] Use the Protein Data Bank PDB website. 10 minutes [2] Use the WebMol Viewer.
More informationProtein Structures: Experiments and Modeling. Patrice Koehl
Protein Structures: Experiments and Modeling Patrice Koehl Structural Bioinformatics: Proteins Proteins: Sources of Structure Information Proteins: Homology Modeling Proteins: Ab initio prediction Proteins:
More informationThe Structure and Functions of Proteins
Wright State University CORE Scholar Computer Science and Engineering Faculty Publications Computer Science and Engineering 2003 The Structure and Functions of Proteins Dan E. Krane Wright State University
More informationBiomolecules: lecture 9
Biomolecules: lecture 9 - understanding further why amino acids are the building block for proteins - understanding the chemical properties amino acids bring to proteins - realizing that many proteins
More informationBiochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015,
Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015, Course,Informa5on, BIOC%530% GraduateAlevel,discussion,of,the,structure,,func5on,,and,chemistry,of,proteins,and, nucleic,acids,,control,of,enzyma5c,reac5ons.,please,see,the,course,syllabus,and,
More informationAnalysis and Prediction of Protein Structure (I)
Analysis and Prediction of Protein Structure (I) Jianlin Cheng, PhD School of Electrical Engineering and Computer Science University of Central Florida 2006 Free for academic use. Copyright @ Jianlin Cheng
More informationMolecular Modelling. part of Bioinformatik von RNA- und Proteinstrukturen. Sonja Prohaska. Leipzig, SS Computational EvoDevo University Leipzig
part of Bioinformatik von RNA- und Proteinstrukturen Computational EvoDevo University Leipzig Leipzig, SS 2011 Protein Structure levels or organization Primary structure: sequence of amino acids (from
More informationHelpful resources for all X ray lectures Crystallization http://www.hamptonresearch.com under tech support: crystal growth 101 literature Spacegroup tables http://img.chem.ucl.ac.uk/sgp/mainmenu.htm Crystallography
More informationStatistical Machine Learning Methods for Bioinformatics IV. Neural Network & Deep Learning Applications in Bioinformatics
Statistical Machine Learning Methods for Bioinformatics IV. Neural Network & Deep Learning Applications in Bioinformatics Jianlin Cheng, PhD Department of Computer Science University of Missouri, Columbia
More informationSupporting Online Material for
www.sciencemag.org/cgi/content/full/309/5742/1868/dc1 Supporting Online Material for Toward High-Resolution de Novo Structure Prediction for Small Proteins Philip Bradley, Kira M. S. Misura, David Baker*
More informationLecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability
Lecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Part I. Review of forces Covalent bonds Non-covalent Interactions Van der Waals Interactions
More information4 Proteins: Structure, Function, Folding W. H. Freeman and Company
4 Proteins: Structure, Function, Folding 2013 W. H. Freeman and Company CHAPTER 4 Proteins: Structure, Function, Folding Learning goals: Structure and properties of the peptide bond Structural hierarchy
More informationProtein structure alignments
Protein structure alignments Proteins that fold in the same way, i.e. have the same fold are often homologs. Structure evolves slower than sequence Sequence is less conserved than structure If BLAST gives
More informationProteins are not rigid structures: Protein dynamics, conformational variability, and thermodynamic stability
Proteins are not rigid structures: Protein dynamics, conformational variability, and thermodynamic stability Dr. Andrew Lee UNC School of Pharmacy (Div. Chemical Biology and Medicinal Chemistry) UNC Med
More informationProtein Structure Basics
Protein Structure Basics Presented by Alison Fraser, Christine Lee, Pradhuman Jhala, Corban Rivera Importance of Proteins Muscle structure depends on protein-protein interactions Transport across membranes
More informationF. Piazza Center for Molecular Biophysics and University of Orléans, France. Selected topic in Physical Biology. Lecture 1
Zhou Pei-Yuan Centre for Applied Mathematics, Tsinghua University November 2013 F. Piazza Center for Molecular Biophysics and University of Orléans, France Selected topic in Physical Biology Lecture 1
More informationMajor Types of Association of Proteins with Cell Membranes. From Alberts et al
Major Types of Association of Proteins with Cell Membranes From Alberts et al Proteins Are Polymers of Amino Acids Peptide Bond Formation Amino Acid central carbon atom to which are attached amino group
More informationBiological Macromolecules
Introduction for Chem 493 Chemistry of Biological Macromolecules Dr. L. Luyt January 2008 Dr. L. Luyt Chem 493-2008 1 Biological macromolecules are the molecules of life allow for organization serve a
More informationUnit 1: Chemistry - Guided Notes
Scientific Method Notes: Unit 1: Chemistry - Guided Notes 1 Common Elements in Biology: Atoms are made up of: 1. 2. 3. In order to be stable, an atom of an element needs a full valence shell of electrons.
More informationProtein Structure Bioinformatics Introduction
1 Swiss Institute of Bioinformatics Protein Structure Bioinformatics Introduction Basel, 27. September 2004 Torsten Schwede Biozentrum - Universität Basel Swiss Institute of Bioinformatics Klingelbergstr
More informationSCOP. all-β class. all-α class, 3 different folds. T4 endonuclease V. 4-helical cytokines. Globin-like
SCOP all-β class 4-helical cytokines T4 endonuclease V all-α class, 3 different folds Globin-like TIM-barrel fold α/β class Profilin-like fold α+β class http://scop.mrc-lmb.cam.ac.uk/scop CATH Class, Architecture,
More informationWeek 10: Homology Modelling (II) - HHpred
Week 10: Homology Modelling (II) - HHpred Course: Tools for Structural Biology Fabian Glaser BKU - Technion 1 2 Identify and align related structures by sequence methods is not an easy task All comparative
More informationThe biomolecules of terrestrial life
Functional groups in biomolecules Groups of atoms that are responsible for the chemical properties of biomolecules The biomolecules of terrestrial life Planets and Astrobiology (2017-2018) G. Vladilo 1
More informationMolecular Modeling. Prediction of Protein 3D Structure from Sequence. Vimalkumar Velayudhan. May 21, 2007
Molecular Modeling Prediction of Protein 3D Structure from Sequence Vimalkumar Velayudhan Jain Institute of Vocational and Advanced Studies May 21, 2007 Vimalkumar Velayudhan Molecular Modeling 1/23 Outline
More informationDetails of Protein Structure
Details of Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Anne Mølgaard, Kemisk Institut, Københavns Universitet Learning Objectives
More information7.91 Amy Keating. Solving structures using X-ray crystallography & NMR spectroscopy
7.91 Amy Keating Solving structures using X-ray crystallography & NMR spectroscopy How are X-ray crystal structures determined? 1. Grow crystals - structure determination by X-ray crystallography relies
More informationX-Ray structure analysis
X-Ray structure analysis Kay Diederichs kay.diederichs@uni-konstanz.de Analysis of what? Proteins ( /ˈproʊˌtiːnz/ or /ˈproʊti.ɨnz/) are biochemical compounds consisting of one or more polypeptides typically
More informationFull file at
MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. 1) Which of the following is an uncharged particle found in the nucleus of 1) an atom and which has
More informationCHEM 463: Advanced Inorganic Chemistry Modeling Metalloproteins for Structural Analysis
CHEM 463: Advanced Inorganic Chemistry Modeling Metalloproteins for Structural Analysis Purpose: The purpose of this laboratory is to introduce some of the basic visualization and modeling tools for viewing
More information1/23/2012. Atoms. Atoms Atoms - Electron Shells. Chapter 2 Outline. Planetary Models of Elements Chemical Bonds
Chapter 2 Outline Atoms Chemical Bonds Acids, Bases and the p Scale Organic Molecules Carbohydrates Lipids Proteins Nucleic Acids Are smallest units of the chemical elements Composed of protons, neutrons
More informationBiochemistry 530: Introduction to Structural Biology. Autumn Quarter 2014 BIOC 530
Biochemistry 530: Introduction to Structural Biology Autumn Quarter 2014 Course Information Course Description Graduate-level discussion of the structure, function, and chemistry of proteins and nucleic
More information2: CHEMICAL COMPOSITION OF THE BODY
1 2: CHEMICAL COMPOSITION OF THE BODY Although most students of human physiology have had at least some chemistry, this chapter serves very well as a review and as a glossary of chemical terms. In particular,
More informationProtein Structure Prediction
Page 1 Protein Structure Prediction Russ B. Altman BMI 214 CS 274 Protein Folding is different from structure prediction --Folding is concerned with the process of taking the 3D shape, usually based on
More informationTemplate Based Protein Structure Modeling Jianlin Cheng, PhD
Template Based Protein Structure Modeling Jianlin Cheng, PhD Professor Department of EECS Informatics Institute University of Missouri, Columbia 2018 Sequence, Structure and Function AGCWY Cell Protein
More informationVisualization of Macromolecular Structures
Visualization of Macromolecular Structures Present by: Qihang Li orig. author: O Donoghue, et al. Structural biology is rapidly accumulating a wealth of detailed information. Over 60,000 high-resolution
More informationBME Engineering Molecular Cell Biology. Structure and Dynamics of Cellular Molecules. Basics of Cell Biology Literature Reading
BME 42-620 Engineering Molecular Cell Biology Lecture 05: Structure and Dynamics of Cellular Molecules Basics of Cell Biology Literature Reading BME42-620 Lecture 05, September 13, 2011 1 Outline Review:
More informationD Dobbs ISU - BCB 444/544X 1
11/7/05 Protein Structure: Classification, Databases, Visualization Announcements BCB 544 Projects - Important Dates: Nov 2 Wed noon - Project proposals due to David/Drena Nov 4 Fri PM - Approvals/responses
More informationWhat is the central dogma of biology?
Bellringer What is the central dogma of biology? A. RNA DNA Protein B. DNA Protein Gene C. DNA Gene RNA D. DNA RNA Protein Review of DNA processes Replication (7.1) Transcription(7.2) Translation(7.3)
More informationThe protein folding problem consists of two parts:
Energetics and kinetics of protein folding The protein folding problem consists of two parts: 1)Creating a stable, well-defined structure that is significantly more stable than all other possible structures.
More informationModel Mélange. Physical Models of Peptides and Proteins
Model Mélange Physical Models of Peptides and Proteins In the Model Mélange activity, you will visit four different stations each featuring a variety of different physical models of peptides or proteins.
More informationProtein Structure: Data Bases and Classification Ingo Ruczinski
Protein Structure: Data Bases and Classification Ingo Ruczinski Department of Biostatistics, Johns Hopkins University Reference Bourne and Weissig Structural Bioinformatics Wiley, 2003 More References
More informationStructure Determination by NMR Spectroscopy #3-1
Structure Determination by NMR Spectroscopy #3-1 3. Computational methods in NMR-spectroscopy 3.1 Nomenclature of proteins and nucleic acids 3.1.1. Classification of structural relationships between molecules
More informationTHE TANGO ALGORITHM: SECONDARY STRUCTURE PROPENSITIES, STATISTICAL MECHANICS APPROXIMATION
THE TANGO ALGORITHM: SECONDARY STRUCTURE PROPENSITIES, STATISTICAL MECHANICS APPROXIMATION AND CALIBRATION Calculation of turn and beta intrinsic propensities. A statistical analysis of a protein structure
More informationLecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability
Lecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Part I. Review of forces Covalent bonds Non-covalent Interactions: Van der Waals Interactions
More informationTeacher Instructions
Teacher Instructions To print handouts for students Go to File print, change Print what: to handouts, change # per page if desired to enlarge slides on page Change Print range to slides and type in slide
More information7.88J Protein Folding Problem Fall 2007
MIT OpenCourseWare http://ocw.mit.edu 7.88J Protein Folding Problem Fall 2007 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms. Lecture Notes - 3 7.24/7.88J/5.48J
More informationChapter 25 Organic and Biological Chemistry
Chapter 25 Organic and Biological Chemistry Organic Chemistry The chemistry of carbon compounds. Carbon has the ability to form long chains. Without this property, large biomolecules such as proteins,
More informationNMR, X-ray Diffraction, Protein Structure, and RasMol
NMR, X-ray Diffraction, Protein Structure, and RasMol Introduction So far we have been mostly concerned with the proteins themselves. The techniques (NMR or X-ray diffraction) used to determine a structure
More informationTemplate Free Protein Structure Modeling Jianlin Cheng, PhD
Template Free Protein Structure Modeling Jianlin Cheng, PhD Associate Professor Computer Science Department Informatics Institute University of Missouri, Columbia 2013 Protein Energy Landscape & Free Sampling
More informationDihedral Angles. Homayoun Valafar. Department of Computer Science and Engineering, USC 02/03/10 CSCE 769
Dihedral Angles Homayoun Valafar Department of Computer Science and Engineering, USC The precise definition of a dihedral or torsion angle can be found in spatial geometry Angle between to planes Dihedral
More informationHomology Modeling (Comparative Structure Modeling) GBCB 5874: Problem Solving in GBCB
Homology Modeling (Comparative Structure Modeling) Aims of Structural Genomics High-throughput 3D structure determination and analysis To determine or predict the 3D structures of all the proteins encoded
More informationGiri Narasimhan. CAP 5510: Introduction to Bioinformatics. ECS 254; Phone: x3748
CAP 5510: Introduction to Bioinformatics Giri Narasimhan ECS 254; Phone: x3748 giri@cis.fiu.edu www.cis.fiu.edu/~giri/teach/bioinfs07.html 2/15/07 CAP5510 1 EM Algorithm Goal: Find θ, Z that maximize Pr
More informationChapter 1 1) Biological Molecules a) Only a small subset of the known elements are found in living systems i) Most abundant- C, N, O, and H ii) Less
Chapter 1 1) Biological Molecules a) Only a small subset of the known elements are found in living systems i) Most abundant- C, N, O, and H ii) Less abundant- Ca, P, K, S, Cl, Na, and Mg b) Cells contain
More informationContents. xiii. Preface v
Contents Preface Chapter 1 Biological Macromolecules 1.1 General PrincipIes 1.1.1 Macrornolecules 1.2 1.1.2 Configuration and Conformation Molecular lnteractions in Macromolecular Structures 1.2.1 Weak
More informationProtein Structure Marianne Øksnes Dalheim, PhD candidate Biopolymers, TBT4135, Autumn 2013
Protein Structure Marianne Øksnes Dalheim, PhD candidate Biopolymers, TBT4135, Autumn 2013 The presentation is based on the presentation by Professor Alexander Dikiy, which is given in the course compedium:
More informationHuman Biology. The Chemistry of Living Things. Concepts and Current Issues. All Matter Consists of Elements Made of Atoms
2 The Chemistry of Living Things PowerPoint Lecture Slide Presentation Robert J. Sullivan, Marist College Michael D. Johnson Human Biology Concepts and Current Issues THIRD EDITION Copyright 2006 Pearson
More informationProtein structures and comparisons ndrew Torda Bioinformatik, Mai 2008
Protein structures and comparisons ndrew Torda 67.937 Bioinformatik, Mai 2008 Ultimate aim how to find out the most about a protein what you can get from sequence and structure information On the way..
More informationPrinciples of Physical Biochemistry
Principles of Physical Biochemistry Kensal E. van Hold e W. Curtis Johnso n P. Shing Ho Preface x i PART 1 MACROMOLECULAR STRUCTURE AND DYNAMICS 1 1 Biological Macromolecules 2 1.1 General Principles
More informationSUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11524 Supplementary discussion Functional analysis of the sugar porter family (SP) signature motifs. As seen in Fig. 5c, single point mutation of the conserved
More informationToday in Astronomy 106: the long molecules of life
Today in Astronomy 106: the long molecules of life Wet chemistry of nucleobases Nuances of polymerization Replication or mass production of nucleic acids Transcription Codons The protein hemoglobin. From
More informationBIOCHEMISTRY GUIDED NOTES - AP BIOLOGY-
BIOCHEMISTRY GUIDED NOTES - AP BIOLOGY- ELEMENTS AND COMPOUNDS - anything that has mass and takes up space. - cannot be broken down to other substances. - substance containing two or more different elements
More information2) Matter composed of a single type of atom is known as a(n) 2) A) element. B) mineral. C) electron. D) compound. E) molecule.
MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. 1) Which of the following is a particle found in the nucleus of an atom and that has no electrical
More informationApril, The energy functions include:
REDUX A collection of Python scripts for torsion angle Monte Carlo protein molecular simulations and analysis The program is based on unified residue peptide model and is designed for more efficient exploration
More informationCh. 2 BASIC CHEMISTRY. Copyright 2010 Pearson Education, Inc.
Ch. 2 BASIC CHEMISTRY Matter and Composition of Matter Definition: Anything that has mass and occupies space Matter is made up of elements An element cannot be broken down by ordinary chemical means Atoms
More informationBiochemistry Prof. S. DasGupta Department of Chemistry Indian Institute of Technology Kharagpur. Lecture - 06 Protein Structure IV
Biochemistry Prof. S. DasGupta Department of Chemistry Indian Institute of Technology Kharagpur Lecture - 06 Protein Structure IV We complete our discussion on Protein Structures today. And just to recap
More informationProblem Set 1
2006 7.012 Problem Set 1 Due before 5 PM on FRIDAY, September 15, 2006. Turn answers in to the box outside of 68-120. PLEASE WRITE YOUR ANSWERS ON THIS PRINTOUT. 1. For each of the following parts, pick
More informationPractice Midterm Exam 200 points total 75 minutes Multiple Choice (3 pts each 30 pts total) Mark your answers in the space to the left:
MITES ame Practice Midterm Exam 200 points total 75 minutes Multiple hoice (3 pts each 30 pts total) Mark your answers in the space to the left: 1. Amphipathic molecules have regions that are: a) polar
More information09/06/25. Computergestützte Strukturbiologie (Strukturelle Bioinformatik) Non-uniform distribution of folds. Scheme of protein structure predicition
Sequence identity Structural similarity Computergestützte Strukturbiologie (Strukturelle Bioinformatik) Fold recognition Sommersemester 2009 Peter Güntert Structural similarity X Sequence identity Non-uniform
More informationCentral Dogma. modifications genome transcriptome proteome
entral Dogma DA ma protein post-translational modifications genome transcriptome proteome 83 ierarchy of Protein Structure 20 Amino Acids There are 20 n possible sequences for a protein of n residues!
More informationHIV protease inhibitor. Certain level of function can be found without structure. But a structure is a key to understand the detailed mechanism.
Proteins are linear polypeptide chains (one or more) Building blocks: 20 types of amino acids. Range from a few 10s-1000s They fold into varying three-dimensional shapes structure medicine Certain level
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Feb 17, 2018 01:16 am GMT PDB ID : 1IFT Title : RICIN A-CHAIN (RECOMBINANT) Authors : Weston, S.A.; Tucker, A.D.; Thatcher, D.R.; Derbyshire, D.J.; Pauptit,
More informationNumber sequence representation of protein structures based on the second derivative of a folded tetrahedron sequence
Number sequence representation of protein structures based on the second derivative of a folded tetrahedron sequence Naoto Morikawa (nmorika@genocript.com) October 7, 2006. Abstract A protein is a sequence
More informationSUPPLEMENTARY INFORMATION
Supplementary Results DNA binding property of the SRA domain was examined by an electrophoresis mobility shift assay (EMSA) using synthesized 12-bp oligonucleotide duplexes containing unmodified, hemi-methylated,
More informationIntroduction to Computational Structural Biology
Introduction to Computational Structural Biology Part I 1. Introduction The disciplinary character of Computational Structural Biology The mathematical background required and the topics covered Bibliography
More informationProcheck output. Bond angles (Procheck) Structure verification and validation Bond lengths (Procheck) Introduction to Bioinformatics.
Structure verification and validation Bond lengths (Procheck) Introduction to Bioinformatics Iosif Vaisman Email: ivaisman@gmu.edu ----------------------------------------------------------------- Bond
More informationPDBe TUTORIAL. PDBePISA (Protein Interfaces, Surfaces and Assemblies)
PDBe TUTORIAL PDBePISA (Protein Interfaces, Surfaces and Assemblies) http://pdbe.org/pisa/ This tutorial introduces the PDBePISA (PISA for short) service, which is a webbased interactive tool offered by
More informationProperties of amino acids in proteins
Properties of amino acids in proteins one of the primary roles of DNA (but not the only one!) is to code for proteins A typical bacterium builds thousands types of proteins, all from ~20 amino acids repeated
More informationBIBC 100. Structural Biochemistry
BIBC 100 Structural Biochemistry http://classes.biology.ucsd.edu/bibc100.wi14 Papers- Dialogue with Scientists Questions: Why? How? What? So What? Dialogue Structure to explain function Knowledge Food
More informationBIOC 530 Fall, 2011 BIOC 530
Fall, 2011 Course Information Course Description Graduate-level discussion of the structure, function, and chemistry of proteins and nucleic acids, control of enzymatic reactions. Please see the course
More informationTHE UNIVERSITY OF MANITOBA. PAPER NO: 409 LOCATION: Fr. Kennedy Gold Gym PAGE NO: 1 of 6 DEPARTMENT & COURSE NO: CHEM 4630 TIME: 3 HOURS
PAPER NO: 409 LOCATION: Fr. Kennedy Gold Gym PAGE NO: 1 of 6 DEPARTMENT & COURSE NO: CHEM 4630 TIME: 3 HOURS EXAMINATION: Biochemistry of Proteins EXAMINER: J. O'Neil Section 1: You must answer all of
More informationProtein Structure Prediction II Lecturer: Serafim Batzoglou Scribe: Samy Hamdouche
Protein Structure Prediction II Lecturer: Serafim Batzoglou Scribe: Samy Hamdouche The molecular structure of a protein can be broken down hierarchically. The primary structure of a protein is simply its
More information