DOCSLIB.ORG

UCSF Chimera Was Developed by the Computer Graphics Laboratory at the University of California, San Francisco, Under Support of NIH Grant P41-RR01081

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
UCSF Chimera Was Developed by the Computer Graphics Laboratory at the University of California, San Francisco, Under Support of NIH Grant P41-RR01081 matrixcopy apply the transformation matrix of one model to another tcolor color using texture map colors UCSF Chimera matrixget write the current transformation matrices to a ®le texture de®ne texture maps and associated colors QUICK REFERENCE GUIDE June 2007 matrixset read and apply transformation matrices from a ®le thickness move the clipping planes in opposite directions minimize energy-minimize structures turn rotate about the X, Y, or Z axis mmaker (matchmaker) align models in sequence, then in 3D vdw* display van der Waals (VDW) surface modelcolor set color at the model level vdwde®ne* set VDW radii Commands modeldisplay* set display at the model level vdwdensity set VDW surface dot density *reverse function Äcommand available move translate along the X, Y, or Z axis version show copyright information and Chimera version movie capture image frames and assemble them into a movie viewdock start ViewDock and load docking results 2dlabels create arbitrary text labels and place them in 2D namesel name and save the current selection wait suspend command processing until motion has stopped ac enable accelerators (keyboard shortcuts) neon create a shadowed stick/tube image (not on Windows) window adjust the view to contain the speci®ed atoms addaa add an amino acid to a peptide C-terminus objdisplay* display graphical objects windowsize adjust the dimensions of the graphics window addcharge assign partial charges to atoms open* read structures and data, execute command ®les write save a molecule model as a PDB ®le addh add hydrogens pdbrun send an annotated PDB ®le to the system shell writesel write a list of the currently selected (or unselected) items alias* create an alias or list aliases push,pop push or pop images on the picture stack x3dsave save the graphical scene as an X3D ®le align align two atoms along the line of sight rainbow color residues, chains, or models over a range angle measure a bond angle or torsion angle rangecolor color over a range according to attribute values Set/Unset Toggle Options bond* add/delete bonds read execute a command ®le, updating the display at the end bondcolor* color bonds independently from atoms represent control the representation of atoms and bonds (wire, autocolor make each newly opened model a unique color bonddisplay control how bond display depends on atom display stick, bs or b+s, sphere or cpk) independent make each model rotate about its own center of mass bondrepr control the representation of bonds (wire, stick) reset restore default or saved orientations instead of the combined center of mass bondzone* make zoning tools use points along bonds ribbackbone* allow display of both ribbon and backbone atoms Set/Unset Value Options brotation make a bond rotatable ribbon* display ribbon cd change the working directory ribcolor* set ribbon color bg_color set background color; value can be any color name center center the view on speci®ed atoms ribrepr control ribbon representation (¯at, edged, rounded) dc_color set depth cue color; value can be any color name chain chain speci®ed atoms, undisplay the others ribscale control ribbon scaling (Chimera default, licorice) chirality report the R/S con®guration of a chiral center rlabel* display residue labels Miscellaneous Operations (Default Settings) clip* move clipping planes rmsd evaluate the RMSD between speci®ed sets of atoms Action¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ Procedure¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ close close a model rock rock about the X, Y or Z axis selection from screen Ctrl-left mouse button cofr* report or change the center of rotation roll roll about the X, Y, or Z axis adding to a selection Shift-Ctrl-left mouse button color* color atoms/bonds, ribbons, labels, and surfaces rotation make a bond rotatable XY-rotation left mouse button when inside the colordef de®ne a new color save save the current Chimera session "spaceball" conic create a shadowed space-®lling image savepos* save the current orientations Z-rotation left mouse button when outside the copy save an image (Chimera graphics or POV-Ray) scale* scale the view "spaceball" defattr assign attribute values to atoms, residues, or models section move the clipping planes in parallel XY-translation middle mouse button delete delete atoms and bonds select* activate models for motion or select atoms Z-translation Ctrl-middle mouse button display* display speci®ed atoms scaling right mouse button or the Side View set* set options (see Set/Unset Options) (below) distance* measure the distance between two atoms setattr* set an attribute to a speci®ed value Preferences Favorites...Preferences echo send text to the Reply Log show* display speci®ed atoms, undisplay the others searching help Help... Search Documentation... ®ndclash* identify clashes and/or contacts sleep pause command processing focus adjust the view and center of rotation source execute a command ®le, updating the display continually freeze stop all motion start start Chimera tools by name Copyright 2007, The Regents of the University of California All Rights Reserved getcrd report untransformed coordinates stereo switch amongst stereo options and mono viewing hbonds* (®ndhbond) identify possible hydrogen bonds stop exit from Chimera help display the manual page for a command surface* calculate and display molecular surfaces intersurf generate and display interface surfaces surfcat (msms cat) group atoms for surface calculations ksdssp determine secondary structure from protein coordinates surfcolor set surface color source label* display atom labels surfrepr (msms repr) control surface representation (solid, mesh, labelopt control the information in atom labels dot) linewidth control the width of lines in the wireframe representation surftransparency* adjust molecular surface transparency load restore a saved Chimera session swapaa mutate amino acid residues longbond* show/hide pseudobonds representing missing segments swapna mutate nucleic acid residues match superimpose two models system send a command to the system shell Atom Speci®cation Symbols @/defaultRadius=rad rad is the default VDW radius #/lineWidth=width width is the wireframe linewidth Symbol Function Usage @/display whether display is enabled at the #/pointSize=size size is the dot size in VDW surfaces ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ atom level # model number # model (integer) #/vdwDensity=density density is the dot density used for VDW @/element=atno atno is the atomic number surfaces #. submodel number #. submodel (integer) ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ : residue : residue (name or number) @/idatmType=type type is the atom type :: residue name :: residue @/label whether the atom is labeled Atom Speci®cation Examples #0 @/label=label label is the text of the atom label :. chain ID :. chain - all atoms in model 0 @ atom name @atom @/labelColor=labcolor labcolor is the color of the atom #3:45-83,90-98 label @. alternate location ID @. alt_loc - residues 45-83 and 90-98 in model 3 @/name=name name is the atom name :lys,arg − range speci®es a range of models, - lysine and arginine residues submodels, or residues @/occupancy=occupancy occupancy is the occupancy :12,14@ca , name separator separates models or residues, @/radius=radius radius is the current radius (may - alpha carbons in residues 12 and 14 ranges of models or residues, or have been changed from the :12:14@ca names of atoms default VDW radius) - all atoms in residue 12 and the alpha carbon in residue 14 * whole wildcard matches whole atom or residue @/serialNumber=n n is the atom serial number in the :.A@ca,c,n,o names, e.g.,:*@CA speci®es the input ®le - peptide backbone atoms in chain A alpha carbons of all residues @/surfaceCategory=catname catname is the category the atom :50.B,.D = partial wildcard matches partial atom or residue belongs to for surface calculation - residue 50 in chain B and all residues in chain D names, e.g., @C= speci®es all purposes (main, ligand, etc.) :12-15,26-28.a,45.b atoms with names beginning with @/surfaceColor=surfcolor surfcolor is the color of the - residues 12-15 in all chains (except het/water), 26-28 in chain A, C atom's molecular surface and 45 in chain B ? single-char wildcard used for atom and residue names @/surfaceDisplay whether molecular surface #0.1-3,5 only, e.g., :G?? selects all display is turned on for the atom - submodels 1-3 of model 0 and all of model 5 residues with three-letter names #0.1-3,.5 beginning with G @/vdw whether VDW surface display is - submodels 1-3 of model 0 and submodel 5 of all models turned on for the atom ; command separator separates multiple commands on ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ligand a single line - any/all residues automatically classi®ed as ligand z< zone speci®er z<zone or zr<zone speci®es all Residue Attributes element.S residues within zone angstroms Usage Description - all sulfur atoms ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ of the indicated atoms, and :/isHelix whether the residue is in an alpha helix @ca/!label and color!=green and color!=red za<zone speci®es all atoms - atoms named CA which are not labeled, and are not green or red (rather than entire residues) :/isHet whether the residue is in PDB HETATM records (or
Load more

Recommended publications
  • Latest Stable Copy and Install It With: Chmod+X Chimera- *.Bin&&./Chimera- *.Bin
    Tangram Suite Documentation Release 0.0.8 InsiliChem Mar 26, 2019 General instructions 1 What is Tangram Suite 3 2 How to install Tangram Suite5 3 General usage 7 4 FAQ & Known issues 9 5 List of Tans 11 6 Tangram BondOrder 13 7 Tangram QMSetup 15 8 Tangram DummyAtoms 17 9 Tangram GAUDIView 19 10 Tangram MMSetup 21 11 Tangram NCIPlot 23 12 Tangram NormalModes 25 13 Tangram OrbiTraj 27 14 Tangram PLIP 29 15 Tangram PoPMuSiCGUI 31 16 Tangram PropKaGUI 33 17 Tangram ReVina 35 18 Tangram SubAlign 37 19 Tangram TalaDraw 39 i ii Tangram Suite Documentation, Release 0.0.8 It’s composed of several independent graphical interfaces and commands for UCSF Chimera. General instructions 1 Tangram Suite Documentation, Release 0.0.8 2 General instructions CHAPTER 1 What is Tangram Suite In progress 3 Tangram Suite Documentation, Release 0.0.8 4 Chapter 1. What is Tangram Suite CHAPTER 2 How to install Tangram Suite 2.1 Install the full Tangram Suite (recommended) 1 - If you don’t have UCSF Chimera installed, download the latest stable copy and install it with: chmod+x chimera- *.bin&&./chimera- *.bin 2 - Download the latest installer from the releases page (Linux and MacOS only) and run it with: bash tangram-*.sh 2.2 Using the conda meta-package Instead of using the Bash installer, you can use conda (if you are already using it) to create a new environment with the tangram metapackage, which will handle all the dependencies. While in alpha, both insilichem channels are needed (the main one and also the dev label): conda create-n tangram-c insilichem/label/dev-c insilichem-c omnia-c rdkit-c ,!conda-forge tangram 2.3 Updating extensions Each extension will check if there’s a new release available every time you launch it.
    [Show full text]
  • 3D-Printing Models for Chemistry
    3D-Printing Models for Chemistry: A Step-by-Step Open-Source Guide for Hobbyists, Corporate ProfessionAls, and Educators and Student in K-12 and Higher Education Poster Elisabeth Grace Billman-Benveniste+, Jacob Franz++, Loredana Valenzano-Slough+* +Department of Chemistry, Michigan Technological University, ++Department of Mechanical Engineering, Michigan Technological University *Corresponding Author References 1. “LulzBot TAZ 5.” LulzBot, 14 Aug. 2018, www.lulzbot.com/store/printers/lulzbot-taz-5 2. Gaussian 16, Revision B.01, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Li, X.; Caricato, M.; Marenich, A. V.; Bloino, J.; Janesko, B. G.; Gomperts, R.; Mennucci, B.; Hratchian, H. P.; Ortiz, J. V.; Izmaylov, A. F.; Sonnenberg, J. L.; Williams-Young, D.; Ding, F.; Lipparini, F.; Egidi, F.; Goings, J.; Peng, B.; Petrone, A.; Henderson, T.; Ranasinghe, D.; ZakrzeWski, V. G.; Gao, J.; Rega, N.; Zheng, G.; Liang, W.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; HasegaWa, J.; Ishida, M.; NakaJima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Throssell, K.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M. J.; Heyd, J. J.; Brothers, E. N.; Kudin, K. N.; Staroverov, V. N.; Keith, T. A.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A. P.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Millam, J. M.; Klene, M.; Adamo, C.; Cammi, R.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Farkas, O.; Foresman, J. B.; Fox, D. J. Gaussian, Inc., Wallingford CT, 2016. 3.
    [Show full text]
  • Development and Application of a Computational Platform for Complex Molecular Design Jaime Rodríguez-Guerra Pedregal
    ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Development and Application of a Computational Platform for Complex Molecular Design a dissertation submitted by Jaime Rodríguez-Guerra Pedregal & directed by Prof. Dr. Jean-Didier Maréchal in fulfillment of the requirements for the degree of Doctor of Biotechnology Tutor: Prof. Dr. Jordi Joan Cairó Badillo Department of Chemical, Biological and Environmental Engineering Universitat Autònoma de Barcelona July 2018 Development and Application of a Computational Platform for Complex Molecular Design a dissertation submitted by & recommended for acceptance by advisor Jaime Rodríguez-Guerra Pedregal Prof. Dr. Jean-Didier Maréchal Tutor: Prof. Dr. Jordi Joan Cairó Badillo Department of Chemical, Biological and Environmental Engineering Universitat Autònoma de Barcelona July 2018 ©2018 – Jaime Rodríguez-Guerra Pedregal Licensed as Creative Commons BY-NC-ND Attribution-NonCommercial-NoDerivs In the beginning, there was nothing. And God said «Let there be light». And there was light. There was still nothing, but you could see it a lot better. —WoodyAllen. Development and Application of a Computational Platform for Complex Molecular Design by Jaime Rodríguez-Guerra Pedregal Abstract In this dissertation, a series of novel computational modeling tools is reported.
    [Show full text]
  • Hands-On Tutorials of Autodock 4 and Autodock Vina
    Hands-on tutorials of AutoDock 4 and AutoDock Vina Pei-Ying Chu (朱珮瑩) Supervisor: Jung-Hsin Lin (林榮信) Research Center for Applied Sciences, Academia Sinica 2018 Frontiers in Computational Drug Design, Academia Sinica, March 16-20, 2018 AutoDock http://autodock.scripps.edu AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock 4 is free and is available under the GNU General Public License. 2 AutoDock Vina http://vina.scripps.edu/ Because the scoring functions used by AutoDock 4 and AutoDock Vina are different and inexact, on any given problem, either program may provide a better result. AutoDock Vina is available under the Apache license, allowing commercial and 3 non-commercial use and redistribution. http://autodock.scripps.edu/downloads These programs were installed on VM. 4 http://mgltools.scripps.edu/ AutoDockTools (ADT) is developed to help set up the docking. ADT is included in MGLTools packages. 5 In general, each docking (AutoDock 4 and/or AutoDock Vina) requires: 1. structure of the receptor (protein), in pdbqt format 2. structure of the ligand (small molecule, drug, etc.) in pdbqt format 3. docking and grid parameters (search space) PDBQT format is very similar to PDB format but it includes partial charges ('Q') and AutoDock 4 (AD4) atom types ('T'). • Preparing the ligand involves ensuring that its atoms are assigned the correct AutoDock4 atom types, adding Gasteiger charges if necessary, merging non-polar hydrogens, detecting aromatic carbons if any, and setting up the 'torsion tree'.
    [Show full text]
  • Mai Muuttunut Pilit Muut Aidi Mini
    MAIMUUTTUNUT US009963689B2 PILIT MUUT AIDI MINI (12 ) United States Patent ( 10 ) Patent No. : US 9 ,963 , 689 B2 Doudna et al. ( 45) Date of Patent: May 8 , 2018 ( 54 ) CASI CRYSTALS AND METHODS OF USE FOREIGN PATENT DOCUMENTS THEREOF WO WO 2013 / 126794 AL 8 / 2013 ( 71 ) Applicant: The Regents of the University of wo WO 2013 / 142578 A19 / 2013 California , Oakland , CA (US ) WO WO 2013 / 176772 A1 11/ 2013 ( 72 ) Inventors : Jennifer A . Doudna , Oakland , CA OTHER PUBLICATIONS (US ) ; Samuel H . Sternberg , Oakland , McPherson , A . Current Approaches to Macromolecular Crystalli CA (US ) ; Martin Jinek , Oakland , CA zation . European Journal of Biochemistry . 1990 . vol . 189 , pp . (US ) ; Fuguo Jiang , Oakland , CA (US ); 1 - 23 . * Emine Kaya , Oakland , CA (US ) ; Kundrot, C . E . Which Strategy for a Protein Crystallization Project ? Cellular Molecular Life Science . 2004 . vol . 61, pp . 525 - 536 . * David W . Taylor, Jr. , Oakland , CA Benevenuti et al. , Crystallization of Soluble Proteins in Vapor (US ) Diffusion for X - ray Crystallography , Nature Protocols , published on - line Jun . 28 , 2007 , 2 ( 7 ) : 1633 - 1651. * ( 73 ) Assignee : THE REGENTS OF THE Cudney R . Protein Crystallization and Dumb Luck . The Rigaku UNIVERSITY OF CALIFORNIA , Journal. 1999 . vol. 16 , No . 1 , pp . 1 - 7 . * Drenth , “ Principles of Protein X - Ray Crystallography ” , 2nd Edi Oakland , CA (US ) tion , 1999 Springer - Verlag New York Inc ., Chapter 1 , p . 1 - 21. * Moon et al . , “ A synergistic approach to protein crystallization : ( * ) Notice : Subject to any disclaimer , the term of this Combination of a fixed -arm carrier with surface entropy reduction ” , patent is extended or adjusted under 35 Protein Science , 2010 , 19 : 901 -913 .
    [Show full text]
  • UCSF Chimera[Mdash]A Visualization System for Exploratory Research And
    UCSF Chimera—A Visualization System for Exploratory Research and Analysis ERIC F. PETTERSEN, THOMAS D. GODDARD, CONRAD C. HUANG, GREGORY S. COUCH, DANIEL M. GREENBLATT, ELAINE C. MENG, THOMAS E. FERRIN Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143-2240 Received 24 February 2004; Accepted 6 May 2004 DOI 10.1002/jcc.20084 Published online in Wiley InterScience (www.interscience.wiley.com). Abstract: The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1605–1612, 2004 Key words: molecular graphics; extensibility; visualization; multiscale modeling; sequence alignment Introduction had not anticipated.
    [Show full text]
  • Functional Behavior of Molecular Baskets and Structure-Activity Studies on Trapping Organophosphorus Nerve Agents in Water
    Functional Behavior of Molecular Baskets and Structure-Activity Studies on Trapping Organophosphorus Nerve Agents in Water DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Yian Ruan Graduate Program in Chemistry The Ohio State University 2014 Dissertation Committee: Jovica D. Badjic, Advisor Christopher M. Hadad Jon R. Parquette Copyright by Yian Ruan 2014 Abstract Molecular recognition is exploited by nature to carry out delicately regulated reactions and form precisely organized structures in living organisms. Enzymes promote reactions by preorganizing substrates and stabilizing transition states in an active site via covalent and non-covalent interactions. Receptor proteins and antibodies can respond selectively to stimuli and trigger subsequent activities. These protein-substrate interactions have been great inspirations for chemists in the design of synthetic receptors as hosts and the study of their molecular recognition properties. Investigation of recognition behaviors can help decipher sub-cellular processes. Moreover, some artificial host-guest complexes have found applications in catalysis, sensing, imaging and drug delivery systems. The Badjic group has developed a family of host molecules called molecular baskets to study the effect of gating on molecular recognition. These baskets possess a cavity formed by a benzene base and phthalimide side walls. Pyridine-based gates close the basket via hydrogen bonds or metal chelation. Tuning the electronic and steric characteristics of gates affects the rate of guests entering and departing the basket. ii With all the knowledge about molecular gating, questions arise as to whether these gates can be applied to other platforms and how the mechanism of gating will be affected.
    [Show full text]
  • Molecular Dynamics (MD) for Cancer Control Protocol
    Molecular Dynamics (MD) for Cancer control Protocol Claudio Nicolini ( [email protected] ) Claudio Ando Nicolini's Lab, NanoWorld, USA; HC Professor Nanobiotechnology, Lomonosov Moscow State University, Russia; Foreign Member Russian Academy of Sciences; President NWI Fondazione EL.B.A. Nicolini; Editor-in-Chief NWJ, Santa Clara, USA Marine Bozdaganyan Claudio Ando Nicolini's Lab, NanoWorld, USA; Lomonosov Moscow State University (MSU), Moscow, Russia; Fondazione EL.B.A. Nicolini Nicola Luigi Bragazzi Claudio Ando Nicolini's Lab, NanoWorld, USA Philippe Orekhov Claudio Ando Nicolini's Lab, NanoWorld, USA Eugenia Pechkova Claudio Ando Nicolini's Lab, NanoWorld, USA Method Article Keywords: Langmuir-Blodgett (LB)-based crystallography Posted Date: March 15th, 2016 DOI: https://doi.org/10.1038/protex.2016.016 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/13 Abstract In the present protocol, we describe how molecular dynamics \(MD) can be applied for studying Langmuir-Blodgett \(LB)-based crystal proteins. MD can therefore play a major role in nanomedicine, as well as in personalized medicine. Introduction The computer simulation of dynamics in molecular systems is widely used in molecular physics, biotechnology, medicine, chemistry and material sciences to predict physical and mechanical properties of new samples of matter. In the molecular dynamics method there is a polyatomic molecular system in which all atoms are interacting like material points, and behavior of the atoms is described by the equations of classical mechanics. This method allows doing simulations of the system of the order of 106 atoms in the time range up to 1 microsecond.
    [Show full text]
  • Eduardo's Guide for 3D Printing Proteins Using Chimera for 3D Printing
    Eduardo’s Guide for 3D Printing Proteins Eduardo da Veiga Beltrame – [email protected] - www.munfred.com ​ ​ ​ Using Chimera for 3D Printing UCSF Chimera is a free and open source molecular visualizer. In this tutorial we’ll show how Chimera can be used to generate 3D printable molecular models for FDM/FFF desktop 3D printers. You can download Chimera at https://www.cgl.ucsf.edu/chimera/. ​ ​ Finding PDB Files First, you need the coordinate file of the molecule you want to print. The files containing the atoms coordinates for a molecule are called .pdb files (for protein data bank). These structures are determined using an array of techniques such as x-ray crystallography and nuclear magnetic resonance, and when they are published they are also deposited in databases and become freely available for download. The biggest such database is the Protein Data Bank, and if you are interested it's worth a visit: www.rcsb.org ​ If you’re looking for cool structures and some explanations, the molecule of the month PDB articles at http://pdb101.rcsb.org/ are a good way to start browsing. They are ​ ​ written by David Goodsell, who is awesome. If you can't find your molecule, if it's not on the PDB it's probably because nobody knows it's structure yet. If what you want is some small molecule, you can try searching for the structure online, or can draw it using Avogadro, a free and open source molecule editor you can get at www.avogadro.cc. ​ ​ Visualizing and Exporting Models Once you have your PDB file, you can render it on a molecular visualizer.
    [Show full text]
  • Visualizing Protein Structures-Tools and Trends
    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 12 January 2020 Visualizing protein structures - tools and trends 1,2 3 1,2 X. Martinez ,​ M. Chavent ,​ M. Baaden ​ ​ ​ 1) CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France 2) Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, Paris, France 3) Institut de Pharmacologie et de Biologie Structurale IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France Abstract Molecular visualisation is fundamental in the current scientific literature, textbooks and dissemination materials, forming an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Visual exploration has become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. Here we first describe a few Swiss Army knives geared towards protein visualisation for everyday use with an existing large user base, then focus on more specialised tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives. Keywords Molecular Graphics, Protein visualization, Software tools, Virtual reality Introduction Many parts of science rely on a visualization-driven cycle of experimentation, reasoning, conjecture and validation, even more so in relation with structural biology and biophysics. Molecular visualization (1) in particular is now broadly used in many contexts, with the purpose of illustration in the scientific literature or the aim to gain insight about primary research data.
    [Show full text]
  • Software and Techniques for Bio-Molecular Modelling
    Software and Techniques for Bio-Molecular Modelling Azat Mukhametov Published by Austin Publications LLC Published Date: December 01, 2016 Online Edition available at http://austinpublishinggroup.com/ebooks For reprints, please contact us at [email protected] All book chapters are Open Access distributed under the Creative Commons Attribution 4.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of the publication. Upon publication of the eBook, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work, identifying the original source. Statements and opinions expressed in the book are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Software and Techniques for Bio-Molecular Modelling | www.austinpublishinggroup.com/ebooks 1 Copyright Mukhametov A.This book chapter is open access distributed under the Creative Commons Attribution 4.0 International License, which allows users to download, copy and build upon published articles even for com- mercial purposes, as long as the author and publisher are properly credited. We consider to publish more books on the topics of drug design, molecular modelling, and structure-activity relationships.
    [Show full text]
  • Opendiscovery: Automated Docking of Ligands to Proteins and Molecular Simulation
    OpenDiscovery: Automated Docking of Ligands to Proteins and Molecular Simulation Gareth Price Computational MiniProject OpenDiscovery Aims + Achievements • Produce a high-throughput protocol to screen a library of chemical compounds against a protein • Use this protocol to produce some putative ligands for chemical synthesis and screening • (Miniproject III) • Paper submitted to ACS JCE • “The use of freely available and Open Source tools for in silico screening in Chemical Biology” • Ground work for OpenDiscovery: • Soon will be found at: www.opendiscovery.org.uk 2 Broad Outline Prepare Files Screen Simulate Parameterise 3 Generating Similar Compounds N SMILES Code CN(C)CCCN1c2ccccc2Sc3ccc(c1)cc13 N Cl Normalise S + Fragment Search against database Give X similar compounds based on Tanimoto distance = 4 character fragments Stepping out of the current chemical “space” 4 SMILES to MOL,MOL2, PDB O HO N[C@@H](Cc1ccc(O)c(O)c1)C(=O)O OH NH2 HO •oBabel is very useful at converting between chemical file formats • and is the most popular tool of choice •Also allows a conformer search, so that the energy minimum can be found • random, weighted or systematic (exhaustive) search •Installs with OBMinimize, an in vacuo minimisation tool 5 PDBQT • Vina actually requires PDBQT • i.e. with atomic coordinates (PDB), partial charges (Q) and atom types (T) • This was achieved by using AutoDock Tools • MGLTools (creators of Vina) provide a python script to do this non- interactively • automate using python/shell scripting • PDBQT files for both receptor and
    [Show full text]