Biomolecular Visualization Software Oznur Tastan Naveena Yanamala oznurmb
Biomolecular Visualization Software Oznur Tastan, Naveena Yanamala oznur+mb 3@cs. cmu. edu naveena@cs. cmu. edu http: //www. cgl. ucsf. edu/chimera/Image. Gallery/ Molecular Biophysics 3: Lecture 4
Outline • A short introduction to biomolecular visualization software • Exercise on VMD • Floppy Inclusions and Rigid Substructure Topograpy (FIRST) • Clus. Pro • Gold • Fast Contact 10/7/2020 Molecular Biophysics 3: Lecture 4 2
What do we need? Visualization • Schematic representation – Atom/Bonds/Secondary Structure. . • • Molecular Surfaces Rotate, translate Color specific parts Labeling residues, atoms, bonds http: //www. cgl. ucsf. edu/chimera/Image. Gallery/ 10/7/2020 Molecular Biophysics 3: Lecture 4 3
What do we need? Analyzing and Editing Structures • • • 10/7/2020 Geometrical measurements (distances, angles) Add hydrogens, find Hbonds Dock our structures Sequence and Structure Alignments Mutate. . Many thing. . Molecular Biophysics 3: Lecture 4 4
Extentibility H-Ras docked ribose monophosphate created by View. Dock Interface between the alpha and beta subunits created by Inter. Surf Created by chimera http: //www. cgl. ucsf. edu/chimera/Image. Gallery/ 10/7/2020 Molecular Biophysics 3: Lecture 4 5
Multiple Sequence/Structure Alignments • Create / Display alignments and associated structures. Information flow between the two Created by chimera http: //www. cgl. ucsf. edu/chimera/ Image. Gallery/ 10/7/2020 Molecular Biophysics 3: Lecture 4 6
10/7/2020 Molecular Biophysics 3: Lecture 4 7
What do we need? • Create Images • Create movies Microflaments The organization of satellite tobacco mosaic virus genome http: //www. cgl. ucsf. edu/chimera 10/7/2020 Molecular Biophysics 3: Lecture 4 8
What do we need? – – – – 10/7/2020 Easy menu options Good documentation Nice graphics Command line language + interactive selections and actions Scripting Language Plugins Space/memory Compatibility with different platforms Molecular Biophysics 3: Lecture 4 9
Available tools Free for academia • • GRASP Xtalview Insight. II (Accelrys) SYBYL® (Tripos) • MIDAS-PLUS • • • VMD Chimera Pymol Protein Explorer / Rasmol Mol • Swiss. PDB Viewer More on http: //molvis. sdsc. edu/visres/molvisfw/titles. jsp http: //www. chantelray. com/admin/Adv. HTML_Upload/dollar%20 sign. jpg 10/7/2020 Molecular Biophysics 3: Lecture 4 10
Links to the common used software • RASMOL / Protein Explorer – http: //www. umass. edu/microbio/rasmol/index 2. htm • Py. MOL – http: //pymol. sourceforge. net • MOLMOL – http: //www. mol. biol. ethz. ch/wuthrich/software/molmol • Chimera (UCSF) – http: //www. cgl. ucsf. edu/chimera/ • VMD (UIUC) – http: //www. ks. uiuc. edu/Research/vmd/ 10/7/2020 Molecular Biophysics 3: Lecture 4 11
VMD • By theoretical biophysics group at the University of Illinois and the Beckman Institute • Runs on Windows, Mac. OSX, and most Unix variants. • Can by scripted with Tcl/Tk or Python. • A selection of scripts for VMD is available at: http: //www. ks. uiuc. edu/Research/vmd/ script_library/ • Documentation and other tutorials are available at: http: //www. ks. uiuc. edu/Research/vmd/current/doc. html 10/7/2020 Molecular Biophysics 3: Lecture 4 12
The Floppy Inclusions and Rigid Substructure Topography (FIRST) - All atom representation of the protein - Fix physically inspired constraints Covalent bond Hydrophobic contact a Chemical bond angle A H D B Hydrogen bond - Build a constraint network and analyze the mechanical stability of the network 10/7/2020 Molecular Biophysics 3: Lecture 4 13
Mutually Rigid Clusters Black denotes flexible residues. Color codes for rigid residues. Same color same cluster. FIRST identifies the mutually rigid cluster of residues. Rader, BLM 2004 10/7/2020 Molecular Biophysics 3: Lecture 4 14
Dilution Plot Primary Sequence Hydrogen bonds are diluted First line initial folded structure rigid cluster composition 10/7/2020 As the protein unfolds, rigid cluster composition changes Molecular Biophysics 3: Lecture 4 15
Let’s go and work in the computer lab! 10/7/2020 Molecular Biophysics 3: Lecture 4 16
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