Using the MMTSB Tool Set
|
|
- Darleen Adams
- 6 years ago
- Views:
Transcription
1 Using the MMTSB Tool Set MMTSB NIH Research Resource PSC Workshop 2003
2 Architecture of MMTSB Tool Set
3 MMTSB Tool Set Package o Available from: (free for academic use) o Includes: Perl packages (.pm) Perl utilities (.pl) External programs (MONSSTER, rebuild, etc.) o Needs: Perl Version or newer Compilers (FORTRAN 77, C++)
4 Supported Platforms o Linux (PC, Alpha) o SGI Irix o DEC OSF/1 o IBM AIX o Sun Solaris o MacOS X o UNIX + Perl + GNU compilers o Windows?
5 Package Installation o Download Tool Set Package (Register!) o Unpack > cd /usr/local/mmtsb > gunzip mmtsb.tar.gz > tar xvf mmtsb.tar o Run install.sh >./install.sh o Set environment setenv MMTSBDIR /usr/local/mmtsb set path = ( $path $MMTSBDIR/perl $MMTSBDIR/bin )
6 External Programs: CHARMM/Amber o CHARMM (c29b, c30a, or newer) setenv CHARMMEXEC /usr/local/bin/charmm.exe setenv CHARMMDATA /usr/local/data/charmm o Amber (Version 7) setenv AMBERHOME /usr/local/amber7 setenv SANDEREXEC /usr/local/bin/sander.exe
7 Other External Programs o SCWRL Version 2.95 (Dunbrack) > cp scwrl $MMTSBDIR/bin o DSSP (Kabsch & Sander) > cp dsspcmbi $MMTSBDIR/bin
8 Using the MMTSB Tool Set Command-line oriented utilities > mincharmm.pl 1vii.pdb with options: > mincharmm.pl par minsteps=100,nocut 1vii.pdb Use MMTSB Packages in new Perl scripts #!/usr/bin/perl use Molecule; my $mol = &Molecule::new(); $mol->readpdb( 1vii.pdb );
9 Input / Output Input usually expected from file name or std input > mincharmm.pl 1vii.pdb > cat 1vii.pdb mincharmm.pl Output usually written to standard output > mincharmm.pl 1vii.pdb > 1vii.min.pdb - can be used for standard input/output > cat 1vii.pdb lsqfit.pl 1vii.min.pdb > mincharmm.pl log 1vii.pdb Command pipes > mincharmm.pl 1vii.pdb mdcharmm.pl
10 All Atom Structure Representation: PDB Formats PDB CHARMM22 CHARMM19 Amber ILE Cd CD1 CD CD CD1 HIS prot Nd HIS HSD HIS HID HIS prot Ne HIS HSE HSD HIE N-terminus 1H/2H/3H HT1/HT2/HT3 HT1/HT2/HT3 H1/H2/H3 C-terminus O/OXT OT1/OT2 OT1/OT2 O/OXT Hydrogens 1HB/2HB HB1/HB2 - HB2/HB3 CYS S-S CYS CYS CYS CYX
11 All Atom Structure Representation: Multiple Chains, Ligands Multiple chains Chain IDs are used to separate chains CHARMM segment IDs are generated automatically HETATM records (solvent, ligands, cofactors) Read into single chain (+) but written out as HETATM Explicit solvent Recognized if residue name TIP3/OH2 and ATOM rec. Disulfides SSBOND entry recognized and kept
12 Parallel Execution Parallelism within CHARMM/Amber: parallel molecular dynamics / minimization tightly coupled, based on MPI setenv CHARMMEXEC mpirun n 8 /usr/local/bin/charmm.exe setenv SANDEREXEC mpirun n 8 /usr/local/bin/sander.exe Parallelism within MMTSB Tool Set ensemble computing, replica exchange simulations TCP/IP socket-based server/client architecture
13 MMTSB Parallel Options: Shared Memory Server Client 1 Client 2 Client 3 > ensrun.pl cpus 4 > aarex.pl temp 4:300:350 use 4 CPUs for 4 clients + server on SMP architecture Client 4
14 MMTSB Parallel Options: Distributed Environment Node 1 Node 2 Server Client 1 Client 2 Client 3 > ensrun.pl cpus 4 hosts hlist > ensrun.pl cpus 4 mp hosts hlist Host file: node1 1 /tmp/mmtsb node2 2 /tmp/mmtsb node3 1 /tmp/mmtsb Node 3 Client 4 uses 4 CPUs on 3 nodes requires rsh to work with.rhosts
15 MMTSB Parallel Options: PSC Environment Jobs are placed on each node with prun Environment variable RMS_RANK contains rank for more than one node: > prun N all ensrun.pl jobenv RMS_RANK saveid id.file node 0 starts server and writes id.file all nodes wait for id.file and connect as clients
16 -help option Help/Documentation > dihed.pl help usage: dihed.pl [options] [refpdb [cmppdb]] options: [-l min:max[...]] [-list phi psi chi1 omega] Online manual pages with examples Tutorials (in progress) support: Mailing List: available soon
17 Utility Functions PDB format and structure manipulation convpdb.pl complete.pl Structure analysis lsqfit.pl, rms.pl dihed.pl contacts.pl rgyr.pl genseq.pl -dssp
18 Conversion between PDB Formats convpdb.pl Generate specific PDB format > convpdb.pl out amber 1vii.pdb ATOM 1 N MET ATOM 2 H1 MET ATOM 3 H2 MET ATOM 4 H3 MET ATOM 5 CA MET ATOM 6 HA MET ATOM 7 CB MET ATOM 8 HB2 MET ATOM 9 HB3 MET > convpdb.pl segnames out charmm22 1vii.pdb ATOM 1 N MET PRO0 ATOM 2 HT1 MET PRO0 ATOM 3 HT2 MET PRO0 ATOM 4 HT3 MET PRO0 ATOM 5 CA MET PRO0
19 Manipulation of PDB Files convpdb.pl Renumber residues > convpdb.pl renumber 5 1vii.pdb ATOM 1 N MET ATOM 2 HT1 MET ATOM 3 HT2 MET ATOM 4 HT3 MET ATOM 5 CA MET Center structure at coordinate origin > convpdb.pl center 1vii.pdb ATOM 1 N MET ATOM 2 HT1 MET ATOM 3 HT2 MET ATOM 4 HT3 MET ATOM 5 CA MET
20 Subselection from PDB Files convpdb.pl Residue subset by number > convpdb.pl sel 10:15 1vii.pdb ATOM 141 N VAL ATOM 142 HN VAL ATOM 143 CA VAL Residue subset by sequence > convpdb.pl selseq VFGMT 1vii.pdb ATOM 141 N VAL ATOM 142 HN VAL ATOM 143 CA VAL NMR model selection > convpdb.pl model 2 1d3z.pdb ATOM 1 N MET A ATOM 2 CA MET A ATOM 3 C MET A
21 Completing All-atom Structures: complete.pl > complete.pl model.pdb ATOM 1 N MET ATOM 2 HT1 MET ATOM 3 HT2 MET ATOM 4 HT3 MET ATOM 5 CA MET Ca Rebuild backbone Ca sufficient, but rebuilds only what is missing Add side chains Add hydrogen atoms
22 Superposition of Structures lsqfit.pl Superposition of entire structure > lsqfit.pl 1vii.pdb 1vii.sample.pdb Superposition of subset > lsqfit.pl l 10:15 1vii.pdb 1vii.sample.pdb > lsqfit.pl x 10:15 1vii.pdb 1vii.sample.pdb Superposition with different sequence > lsqfit.pl resnumonly l 10:15 1vii.pdb helix.pdb
23 Comparison of Different Conformations rms.pl Coordinate RMSD with respect to reference > rms.pl out CA fit 1vii.pdb 1vii.sample.pdb CA > rms.pl l 10:15 fitxl 1vii.pdb 1vii.sample.pdb > rms.pl fitl 10:15 1vii.pdb 1vii.sample.pdb Other possible values: CA, CB, CAB, heavy, all,
24 Peptide Dihedral Angles: dihed.pl Calculate f/y/w/c 1 dihedral angles > dihed.pl list phi,psi,omega,chi1 1vii.pdb MET1: LEU2: SER3: Calculate dihedral RMSD > dihed.pl 1vii.pdb 1vii.sample.pdb phi: ( % ), psi: ( % ), chi1: ( % ) c 1
25 Side Chain Contacts: contact.pl List side chain contacts (min. distance < 4.2 Å) > contact.pl list 1vii.pdb Compare contacts to reference > contact.pl 1vii.pdb 1vii.sample.pdb 15 contacts ( fraction: ), rho:
26 Radius of Gyration: rgyr.pl > rgyr.pl 1vii.pdb > rgyr.pl caonly 1vii.pdb c = N r g  i 1 = N r  i i (r i - 2 c)
27 Secondary Structure Analysis: genseq.pl -dssp > genseq.pl out onesec -dssp 1vii.pdb MLSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLF UUUHHHHHUUUUUUHHHHUUUUHHHHHHHHHHUUUU Secondary structure identified from hydrogen bonding: H helical (a) E extended (b) U random coil/undefined
MMTSB Toolset. Michael Feig MMTSB/CTBP 2006 Summer Workshop. MMTSB/CTBP Summer Workshop Michael Feig, 2006.
MMTSB Toolset Michael Feig MMTSB/CTBP 2006 Summer Workshop MMTSB Tool Set Overview application programs Perl libraries Perl utilities MMTSB Tool Set Functionality Structure manipulation and analysis Classical
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 informationMolecular modeling with InsightII
Molecular modeling with InsightII Yuk Sham Computational Biology/Biochemistry Consultant Phone: (612) 624 7427 (Walter Library) Phone: (612) 624 0783 (VWL) Email: shamy@msi.umn.edu How to run InsightII
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 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 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 informationUser Guide for LeDock
User Guide for LeDock Hongtao Zhao, PhD Email: htzhao@lephar.com Website: www.lephar.com Copyright 2017 Hongtao Zhao. All rights reserved. Introduction LeDock is flexible small-molecule docking software,
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 informationComputational Analysis of Small Proteins using the WebAmber Interface. By Eddie Gorr Gustavus Adolphus College
Computational Analysis of Small Proteins using the WebAmber Interface By Eddie Gorr Gustavus Adolphus College Research Goals Upgrade And Revise Web-based Amber interface Use Amber to Explore Interactions
More informationContinuous Constant ph Molecular Dynamics
Continuous Constant ph Molecular Dynamics Ana Patricia Gámiz-Hernández Department of Chemistry University of Basel AG Meuwly apgamiz (UniBas) CPHMD July 2013 1 / 46 Outline 1 Motivation Biopolymers in
More informationPortal. User Guide Version 1.0. Contributors
Portal www.dockthor.lncc.br User Guide Version 1.0 Contributors Diogo A. Marinho, Isabella A. Guedes, Eduardo Krempser, Camila S. de Magalhães, Hélio J. C. Barbosa and Laurent E. Dardenne www.gmmsb.lncc.br
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 informationLysinebasedTrypsinActSite. A computer application for modeling Chymotrypsin
LysinebasedTrypsinActSite A computer application for modeling Chymotrypsin Version.2 May 2006 LysTAS A computer application for modeling chymotrypsin Version.2 May 2006 Table of Contents Page. Introduction
More informationComputational Structural Biology and Molecular Simulation. Introduction to VMD Molecular Visualization and Analysis
Computational Structural Biology and Molecular Simulation Introduction to VMD Molecular Visualization and Analysis Emad Tajkhorshid Department of Biochemistry, Beckman Institute, Center for Computational
More informationPhysiochemical Properties of Residues
Physiochemical Properties of Residues Various Sources C N Cα R Slide 1 Conformational Propensities Conformational Propensity is the frequency in which a residue adopts a given conformation (in a polypeptide)
More informationSecondary and sidechain structures
Lecture 2 Secondary and sidechain structures James Chou BCMP201 Spring 2008 Images from Petsko & Ringe, Protein Structure and Function. Branden & Tooze, Introduction to Protein Structure. Richardson, J.
More informationSupporting information to: Time-resolved observation of protein allosteric communication. Sebastian Buchenberg, Florian Sittel and Gerhard Stock 1
Supporting information to: Time-resolved observation of protein allosteric communication Sebastian Buchenberg, Florian Sittel and Gerhard Stock Biomolecular Dynamics, Institute of Physics, Albert Ludwigs
More informationWhat makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces: Electronic Supplementary
Electronic Supplementary Material (ESI) for Journal of Materials Chemistry B. This journal is The Royal Society of Chemistry 21 What makes a good graphene-binding peptide? Adsorption of amino acids and
More informationFigure 1. Molecules geometries of 5021 and Each neutral group in CHARMM topology was grouped in dash circle.
Project I Chemistry 8021, Spring 2005/2/23 This document was turned in by a student as a homework paper. 1. Methods First, the cartesian coordinates of 5021 and 8021 molecules (Fig. 1) are generated, in
More informationTutorial I: IQ MOL and Basic DFT and MP2 Calculations 1 / 30
Tutorial I: IQ MOL and Basic DFT and MP2 Calculations Q-Chem User Workshop, Denver March 21, 2015 1 / 30 2 / 30 Introduction to IQMOL DFT and MP2 Calculations 3 / 30 IQMOL and Q-CHEM IQMOL is an open-source
More information1. Protein Data Bank (PDB) 1. Protein Data Bank (PDB)
Protein structure databases; visualization; and classifications 1. Introduction to Protein Data Bank (PDB) 2. Free graphic software for 3D structure visualization 3. Hierarchical classification of protein
More informationProtein Structure Prediction and Display
Protein Structure Prediction and Display Goal Take primary structure (sequence) and, using rules derived from known structures, predict the secondary structure that is most likely to be adopted by each
More informationHands-on Course in Computational Structural Biology and Molecular Simulation BIOP590C/MCB590C. Course Details
Hands-on Course in Computational Structural Biology and Molecular Simulation BIOP590C/MCB590C Emad Tajkhorshid Center for Computational Biology and Biophysics Email: emad@life.uiuc.edu or tajkhors@uiuc.edu
More informationMULTIDOCK V1.0. Richard M. Jackson Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln s Inn Fields London WC2A 3PX
MULTIDOCK V1.0 Richard M. Jackson Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln s Inn Fields London WC2A 3PX 1.0 Description The program MULTIDOCK was developed to provide
More informationProtein Structure Prediction
Protein Structure Prediction Michael Feig MMTSB/CTBP 2006 Summer Workshop From Sequence to Structure SEALGDTIVKNA Ab initio Structure Prediction Protocol Amino Acid Sequence Conformational Sampling to
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 informationSection III - Designing Models for 3D Printing
Section III - Designing Models for 3D Printing In this section of the Jmol Training Guide, you will become familiar with the commands needed to design a model that will be built on a 3D Printer. As you
More informationNMR-Structure determination with the program CNS
NMR-Structure determination with the program CNS Blockkurs 2013 Exercise 11.10.2013, room Mango? 1 NMR-Structure determination - Overview Amino acid sequence Topology file nef_seq.mtf loop cns_mtf_atom.id
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 informationAnalysis of MD trajectories in GROMACS David van der Spoel
Analysis of MD trajectories in GROMACS David van der Spoel What does MD produce? Energy terms E(t) Coordinates x(t) Velocities v(t) Forces f(t) Managing your files trjcat - merging trajectories concatenating
More informationGet familiar with PDBsum and the PDB Extract atomic coordinates from protein data files Compute bond angles and dihedral angles
CS483 Assignment #2 Due date: Mar. 1 at the start of class. Protein Geometry Bedbug spit? Just say NO! Purpose of this assignment Get familiar with PDBsum and the PDB Extract atomic coordinates from protein
More informationBuild_model v User Guide
Build_model v.2.0.1 User Guide MolTech Build_model User Guide 2008-2011 Molecular Technologies Ltd. www.moltech.ru Please send your comments and suggestions to contact@moltech.ru. Table of Contents Input
More informationFORSCHUNGSZENTRUM JÜLICH GmbH Zentralinstitut für Angewandte Mathematik D Jülich, Tel. (02461)
FORSCHUNGSZENTRUM JÜLICH GmbH Zentralinstitut für Angewandte Mathematik D-52425 Jülich, Tel. (02461) 61-6402 Interner Bericht Thermalization of Large Fluid Systems consisting of Lennard-Jones Mitures Matthias
More informationPart 7 Bonds and Structural Supports
Part 7 Bonds and Structural Supports http://cbm.msoe.edu/newwebsite/learntomodel Introduction In addition to covalent bonds between atoms in a molecule, Jmol has the ability to render Hydrogen Bonds and
More informationBonds and Structural Supports
Bonds and Structural Supports Part of the Jmol Training Guide from the MSOE Center for BioMolecular Modeling Interactive version available at http://cbm.msoe.edu/teachingresources/jmol/jmoltraining/struts.html
More informationPreparing a PDB File
Figure 1: Schematic view of the ligand-binding domain from the vitamin D receptor (PDB file 1IE9). The crystallographic waters are shown as small spheres and the bound ligand is shown as a CPK model. HO
More informationComputer simulations of protein folding with a small number of distance restraints
Vol. 49 No. 3/2002 683 692 QUARTERLY Computer simulations of protein folding with a small number of distance restraints Andrzej Sikorski 1, Andrzej Kolinski 1,2 and Jeffrey Skolnick 2 1 Department of Chemistry,
More informationForce Fields for Classical Molecular Dynamics simulations of Biomolecules. Emad Tajkhorshid
Force Fields for Classical Molecular Dynamics simulations of Biomolecules Emad Tajkhorshid Theoretical and Computational Biophysics Group, Beckman Institute Departments of Biochemistry and Pharmacology,
More informationStatistically Based Reduced Representation of Amino Acid Side Chains
J. Chem. Inf. Comput. Sci. 2004, 44, 817-830 817 Statistically Based Reduced Representation of Amino Acid Side Chains Jan K. Rainey and M. Cynthia Goh* Department of Chemistry, University of Toronto, Toronto,
More informationStructure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase Cwc27
Acta Cryst. (2014). D70, doi:10.1107/s1399004714021695 Supporting information Volume 70 (2014) Supporting information for article: Structure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase
More informationCan a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?
Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water? Ruhong Zhou 1 and Bruce J. Berne 2 1 IBM Thomas J. Watson Research Center; and 2 Department of Chemistry,
More informationA Brief Guide to All Atom/Coarse Grain Simulations 1.1
A Brief Guide to All Atom/Coarse Grain Simulations 1.1 Contents 1. Introduction 2. AACG simulations 2.1. Capabilities and limitations 2.2. AACG commands 2.3. Visualization and analysis 2.4. AACG simulation
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 informationPotential Energy (hyper)surface
The Molecular Dynamics Method Thermal motion of a lipid bilayer Water permeation through channels Selective sugar transport Potential Energy (hyper)surface What is Force? Energy U(x) F = " d dx U(x) Conformation
More informationProtein Structure Determination Using NMR Restraints BCMB/CHEM 8190
Protein Structure Determination Using NMR Restraints BCMB/CHEM 8190 Programs for NMR Based Structure Determination CNS - Brünger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve,
More informationThe TEN Package. User Guide
================================================================= The TEN Package Tools for Elastic Networks User Guide Lars Ackermann, Silke A. Wieninger and G. Matthias Ullmann =================================================================
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 informationApplications of Molecular Dynamics
June 4, 0 Molecular Modeling and Simulation Applications of Molecular Dynamics Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo Tohru
More information2008 Biowerkzeug Ltd.
2008 Biowerkzeug Ltd. 1 Contents Summary...3 1 Simulation...4 1.1 Setup...4 1.2 Output...4 2 Settings...5 3 Analysis...9 3.1 Setup...9 3.2 Input options...9 3.3 Descriptions...10 Please note that we cannot
More informationOxygen Binding in Hemocyanin
Supporting Information for Quantum Mechanics/Molecular Mechanics Study of Oxygen Binding in Hemocyanin Toru Saito and Walter Thiel* Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470
More informationSupplementary Figure 3 a. Structural comparison between the two determined structures for the IL 23:MA12 complex. The overall RMSD between the two
Supplementary Figure 1. Biopanningg and clone enrichment of Alphabody binders against human IL 23. Positive clones in i phage ELISA with optical density (OD) 3 times higher than background are shown for
More informationExam I Answer Key: Summer 2006, Semester C
1. Which of the following tripeptides would migrate most rapidly towards the negative electrode if electrophoresis is carried out at ph 3.0? a. gly-gly-gly b. glu-glu-asp c. lys-glu-lys d. val-asn-lys
More informationSwissSidechain - Documentation
SwissSidechain - Documentation David Gfeller Swiss Institute of Bioinformatics 1015 Lausanne 13 august 2012 david.gfeller@isb- sib.ch Table of contents 1. Introduction 3 2. Content of the database 3 2.1
More informationPROTEIN'STRUCTURE'DETERMINATION'
PROTEIN'STRUCTURE'DETERMINATION' USING'NMR'RESTRAINTS' BCMB/CHEM'8190' Programs for NMR Based Structure Determination CNS - Brünger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve,
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 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 informationANALYZE. A Program for Cluster Analysis and Characterization of Conformational Ensembles of Polypeptides
ANALYZE A Program for Cluster Analysis and Characterization of Conformational Ensembles of Polypeptides Calculations of conformational characteristics, such as hydrogen bonds, turn position and types,
More informationSecondary Structure. Bioch/BIMS 503 Lecture 2. Structure and Function of Proteins. Further Reading. Φ, Ψ angles alone determine protein structure
Bioch/BIMS 503 Lecture 2 Structure and Function of Proteins August 28, 2008 Robert Nakamoto rkn3c@virginia.edu 2-0279 Secondary Structure Φ Ψ angles determine protein structure Φ Ψ angles are restricted
More informationDock Ligands from a 2D Molecule Sketch
Dock Ligands from a 2D Molecule Sketch March 31, 2016 Sample to Insight CLC bio, a QIAGEN Company Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.clcbio.com support-clcbio@qiagen.com
More informationProtein structure analysis. Risto Laakso 10th January 2005
Protein structure analysis Risto Laakso risto.laakso@hut.fi 10th January 2005 1 1 Summary Various methods of protein structure analysis were examined. Two proteins, 1HLB (Sea cucumber hemoglobin) and 1HLM
More informationVMD: Visual Molecular Dynamics. Our Microscope is Made of...
VMD: Visual Molecular Dynamics Computational Microscope / Tool to Think amino acid tyrosine enzymatic control BPTI VMD tutorial traficking Ubiquitin case study http://www.ks.uiuc.edu/training/casestudies/
More informationRamachandran Plot. 4ysz Phi (degrees) Plot statistics
B Ramachandran Plot ~b b 135 b ~b ~l l Psi (degrees) 5-5 a A ~a L - -135 SER HIS (F) 59 (G) SER (B) ~b b LYS ASP ASP 315 13 13 (A) (F) (B) LYS ALA ALA 315 173 (E) 173 (E)(A) ~p p ~b - -135 - -5 5 135 (degrees)
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 informationViewing and Analyzing Proteins, Ligands and their Complexes 2
2 Viewing and Analyzing Proteins, Ligands and their Complexes 2 Overview Viewing the accessible surface Analyzing the properties of proteins containing thousands of atoms is best accomplished by representing
More informationMolecular Visualization. Introduction
Molecular Visualization Jeffry D. Madura Department of Chemistry & Biochemistry Center for Computational Sciences Duquesne University Introduction Assessments of change, dynamics, and cause and effect
More informationNitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein
Acta Cryst. (2015). D71, 274-282, doi:10.1107/s1399004714025243 Supporting information Volume 71 (2015) Supporting information for article: Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08
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 informationMolecular Modeling Lecture 7. Homology modeling insertions/deletions manual realignment
Molecular Modeling 2018-- Lecture 7 Homology modeling insertions/deletions manual realignment Homology modeling also called comparative modeling Sequences that have similar sequence have similar structure.
More information1 Introduction. command intended for command prompt
Guest Lecture, Smith College, CS 334, BioInformatics 21 October 2008 GROMACS, Position Restrained MD, Protein Catalytic Activity Filip Jagodzinski 1 Introduction GROMACS (GROningen MAchine for Chemistry
More informationElectronic Supplementary Information
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 28 Electronic Supplementary Information ph-dependent Cooperativity and Existence of
More informationProtein Structure and Visualisation. Introduction to PDB and PyMOL
Protein Structure and Visualisation Introduction to PDB and PyMOL 1 Feedback Persons http://www.bio-evaluering.dk/ 2 Program 8.00-8.15 Quiz results 8.15-8.50 Introduction to PDB & PyMOL 8.50-9.00 Break
More informationWRF Modeling System Overview
WRF Modeling System Overview Jimy Dudhia What is WRF? WRF: Weather Research and Forecasting Model Used for both research and operational forecasting It is a supported community model, i.e. a free and shared
More informationPrediction and refinement of NMR structures from sparse experimental data
Prediction and refinement of NMR structures from sparse experimental data Jeff Skolnick Director Center for the Study of Systems Biology School of Biology Georgia Institute of Technology Overview of talk
More informationForce Fields for Classical Molecular Dynamics simulations of Biomolecules. Emad Tajkhorshid
Force Fields for Classical Molecular Dynamics simulations of Biomolecules Emad Tajkhorshid Beckman Institute Departments of Biochemistry Center for Biophysics and Computational Biology University of Illinois
More informationLysozyme pka example - Software. APBS! >!Examples! >!pka calculations! >! Lysozyme pka example. Background
Software Search this site Home Announcements An update on mailing lists APBS 1.2.0 released APBS 1.2.1 released APBS 1.3 released New APBS 1.3 Windows Installer PDB2PQR 1.7.1 released PDB2PQR 1.8 released
More informationAssignment 1: Molecular Mechanics (PART 1 25 points)
Chemistry 380.37 Fall 2015 Dr. Jean M. Standard August 19, 2015 Assignment 1: Molecular Mechanics (PART 1 25 points) In this assignment, you will perform some molecular mechanics calculations using the
More informationThe Molecular Dynamics Method
H-bond energy (kcal/mol) - 4.0 The Molecular Dynamics Method Fibronectin III_1, a mechanical protein that glues cells together in wound healing and in preventing tumor metastasis 0 ATPase, a molecular
More informationDATE A DAtabase of TIM Barrel Enzymes
DATE A DAtabase of TIM Barrel Enzymes 2 2.1 Introduction.. 2.2 Objective and salient features of the database 2.2.1 Choice of the dataset.. 2.3 Statistical information on the database.. 2.4 Features....
More informationPacking of Secondary Structures
7.88 Lecture Notes - 4 7.24/7.88J/5.48J The Protein Folding and Human Disease Professor Gossard Retrieving, Viewing Protein Structures from the Protein Data Base Helix helix packing Packing of Secondary
More informationTridip Sheet, Raja Banerjee*
Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2016 Supplementary information The C NN motif: an intrinsic lover of sulfate and phosphate ions
More informationThe Schrödinger KNIME extensions
The Schrödinger KNIME extensions Computational Chemistry and Cheminformatics in a workflow environment Jean-Christophe Mozziconacci Volker Eyrich Topics What are the Schrödinger extensions? Workflow application
More informationHow is molecular dynamics being used in life sciences? Davide Branduardi
How is molecular dynamics being used in life sciences? Davide Branduardi davide.branduardi@schrodinger.com Exploring molecular processes with MD Drug discovery and design Protein-protein interactions Protein-DNA
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 informationBioinformatics III Structural Bioinformatics and Genome Analysis Part Protein Secondary Structure Prediction. Sepp Hochreiter
Bioinformatics III Structural Bioinformatics and Genome Analysis Part Protein Secondary Structure Prediction Institute of Bioinformatics Johannes Kepler University, Linz, Austria Chapter 4 Protein Secondary
More informationProgramme Last week s quiz results + Summary Fold recognition Break Exercise: Modelling remote homologues
Programme 8.00-8.20 Last week s quiz results + Summary 8.20-9.00 Fold recognition 9.00-9.15 Break 9.15-11.20 Exercise: Modelling remote homologues 11.20-11.40 Summary & discussion 11.40-12.00 Quiz 1 Feedback
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 informationProtein Modeling Methods. Knowledge. Protein Modeling Methods. Fold Recognition. Knowledge-based methods. Introduction to Bioinformatics
Protein Modeling Methods Introduction to Bioinformatics Iosif Vaisman Ab initio methods Energy-based methods Knowledge-based methods Email: ivaisman@gmu.edu Protein Modeling Methods Ab initio methods:
More informationMolecular Dynamics Flexible Fitting
Molecular Dynamics Flexible Fitting Ryan McGreevy Research Programmer University of Illinois at Urbana-Champaign NIH Resource for Macromolecular Modeling and Bioinformatics Molecular Dynamics Flexible
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 informationOnline Protein Structure Analysis with the Bio3D WebApp
Online Protein Structure Analysis with the Bio3D WebApp Lars Skjærven, Shashank Jariwala & Barry J. Grant August 13, 2015 (updated November 17, 2016) Bio3D1 is an established R package for structural bioinformatics
More informationTOPOLOGY FILE TUTORIAL
University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology Theoretical and Computational Biophysics Group TOPOLOGY FILE TUTORIAL Aaron Oakley Timothy Isgro Yi Wang
More informationSupplemental Information for: Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion and Orientation
Supplemental Information for: Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion and Orientation Javier L. Baylon, Ivan L. Lenov, Stephen G. Sligar and Emad Tajkhorshid
More informationStructure of the HIV-1 Capsid Assembly by a hybrid approach
Structure of the HIV-1 Capsid Assembly by a hybrid approach Juan R. Perilla juan@ks.uiuc.edu Theoretical and Computational Biophysics Group University of Illinois at Urbana-Champaign Virion HIV infective
More informationCourse in Applied Structural Bioinformatics: Amber Tutorial
Course in Applied Structural Bioinformatics: Amber Tutorial Lars Skjaerven, Yvan Strahm, Kjell Petersen and Ross Walker September 8, 2010 http://www.bccs.uni.no/ http://www.bioinfo.no/ Contents 1 Introduction
More informationThe Force Field Toolkit (fftk)
Parameterizing Small Molecules Using: The Force Field Toolkit (fftk) Christopher G. Mayne, Emad Tajkhorshid Beckman Institute for Advanced Science and Technology University of Illinois, Urbana-Champaign
More informationProtein Modeling. Generating, Evaluating and Refining Protein Homology Models
Protein Modeling Generating, Evaluating and Refining Protein Homology Models Troy Wymore and Kristen Messinger Biomedical Initiatives Group Pittsburgh Supercomputing Center Homology Modeling of Proteins
More informationComputational Molecular Modeling
Computational Molecular Modeling Lecture 1: Structure Models, Properties Chandrajit Bajaj Today s Outline Intro to atoms, bonds, structure, biomolecules, Geometry of Proteins, Nucleic Acids, Ribosomes,
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 informationSupplemental Materials for. Structural Diversity of Protein Segments Follows a Power-law Distribution
Supplemental Materials for Structural Diversity of Protein Segments Follows a Power-law Distribution Yoshito SAWADA and Shinya HONDA* National Institute of Advanced Industrial Science and Technology (AIST),
More informationMolecular modeling. A fragment sequence of 24 residues encompassing the region of interest of WT-
SUPPLEMENTARY DATA Molecular dynamics Molecular modeling. A fragment sequence of 24 residues encompassing the region of interest of WT- KISS1R, i.e. the last intracellular domain (Figure S1a), has been
More information