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Program (on Mac) to show 3D protein structures?

Program (on Mac) to show 3D protein structures?


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I have an assignment for 6th grade biology. I have to look at a 3D structure of a protein and manipulate it so it only shows the AA I'm interested in currently.

what I already did I already looked up the programs most used for this and they point me to JMol and Yasara but the download files are .bin files and the like and I don't I don't understand which file is the one I should download and how to install it.

Can someone help me please ?


Jmol: how to install

Here are instructions for getting Jmol to run on a Mac (or with a slight variation in the runtime file you need to download and the security warnings, on a PC).

  1. Download Jmol from
    https://sourceforge.net/projects/jmol/files/latest/download?source=files
  2. The name of the file will be something likeJmol-14.29.16-binary.zip. Double-click to unzip.
  3. The unzipped folder has a confusing variety of files. This is because most are used for setting up web pages with Jmol embedded. However there is a double-clickable desktop application without any icon and the unpromising name of:Jmol.jar. When you double-click to launch it you will most likely get a message as shown below (1):

To get round this you must either control-click or right-click and select 'Open With > Jar Launcher as shown above (2).

Click 'Open'. (Next time it will just launch without right-clicking.)

  1. Now, in my case the program launches because I have the Java runtime installed on my machines, but you will probably have to download and install this.
  2. Go to the Oracle Java website athttp://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
    Download and install the appropriate Java SE Runtime Environment, e.gjre-8u172-macosx-x64.dmg

  3. Try launching jmol.jar again. It should work this time.

Jmol: how to use

Because of their emphasis on Jmol in relation to the web, the developers of Jmol do not provide an easy entry to the desktop program. However you can find a clearly illustrated series of web tutorials at the MSOI Centre for Biomoleclar Modelling. I'd highly recommend this as a starting guide.

Although I am not going to describe how you can visualize particular amino acids as that is part of the poster's project and can be found in the instructions. there are a couple of pointers I would make about things that are not entirely obvious.

  1. After you have loaded a protein from the file menu, you will probably want to change its representation, not least because it may be surrounded by red balls (oxygens from water). To do this you need to right click (or click on the Jmol text on the bottom right) and go through two levels of submenus to select an appropriate representation, as shown.

  1. In order to make the selections you require you will need to issue commands in the 'Console'. This can be selected from the File menu:


You could use an online molecular viewer for this. A fairly complete list is available in Wikipedia as well as in JMol wiki.

In particular, JMol that you tried to install has also a JavaScript version called JSMol that you can use on any website that embeds JSMol: RCSB, Proteopedia, a JSMol tutorial, and many more. To load own structure in JSMol: right click and select File > Load > Open Local File.

If you'd prefer a desktop program, there is also plenty of them: JMol, PyMOL, Chimera, VMD, CCP4mg, etc. All of these are free for non-commercial use (some are even free for commercial use) and work on Mac.

The most popular file format for storing 3D structures of protein is the PDB format. If you would not be able to make your viewer of choice to show only the amino-acids you want, you can always open the PDB file in a text editor and remove lines (atoms) that you don't need.


LiteMol Viewer, an HTML5 web application for 3D visualization of molecules and other related data.


Avogadro has a mac version you can use. https://avogadro.cc/

I found it simple.

edit:

You can view the protein you listed here, maybe? ( I am on windows so I do not know if this web app works perfect on mac OS)

https://www.ncbi.nlm.nih.gov/Structure/pdb/1C9O

then in the bottom left corner of the structure image box, there will be a small box icon with arrow.

.

Then you can click on View Sequences and Annotations, under the window tab.

You can then click on the details tab and then left click and drag on the Amino acid sequence to highlight them on the sequence and where they are on the corresponding structure.


3.8: View 3D Animated Images of Proteins in the NCBI Database

  • Contributed by Gerald Bergtrom
  • Professor Emeritus (Biosciences) at University of Wisconsin-Milwaukee

We can&rsquot see them with our own eyes, but viewed by X-Ray diffraction, proteins exhibit exquisite diversity. You can get an X-Ray eye&rsquos view of protein structures at National Center for Biological Information&rsquos Cn3D database. Here&rsquos how to access three- dimensional animated images of proteins from the database:

Click http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dinstall.shtml to download the Cn3D-4.3.1_setup file (for Windows or Mac). The software will reside on your computer and will activate when you go to a macromolecule database search site.

Click View in Cn3D for the desired protein. For human insulin see this:

To rotate the molecule, click View then Animation, then Spin&hellip and enjoy!


The recommended way to cite Jmol is:
Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/

Remember to always use uppercase 'J', lowercase 'mol' (explanation).

If you prefer, a list of articles that describe Jmol can be found in the Jmol Literature section of the Jmol Wiki.

Samples

Check out the Screenshot Gallery (still images) to see samples of what can be done with Jmol
and the Demonstration pages to see buttons and menus in action (interactive object within the webpage).

Features

  • Free, open-source software licensed under the GNU Lesser General Public License
  • HTML5 object, application, and systems integration component
    • JSmol is a web browser object that can be integrated into web pages. It is ideal for development of web-based courseware and web-accessible chemical databases. .
    • The Jmol application is a standalone Java application that runs on the desktop.
    • The JmolViewer can be integrated as a component into other Java applications.
    • Translated into multiple languages: Basque (eu), Brazilian Portuguese (pt_BR), Catalan (ca), Chinese (both zh_CN and zh_TW), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Hungarian (hu), Indonesian (id), Italian (it), Japanese (jp), Korean (ko), Malayan (ms), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), Ukrainian (uk), in addition to the native American English (en-US) and British English (en-GB).
    • Automatically adopts the language of the user's operating system, if it is among the translations available. You can change to another language if desired.
    • For up-to-date details or instructions for adding your language, see the Wiki.
    • Windows
    • Mac OS X
    • Linux / Unix
    • distance
    • angle
    • torsion angle

    What the critics are saying


    This method predicts protein structures when the structural information of similar proteins is not available. The protein structures are built from scratch by calculating the most favorable energy conformations. This method should only be used as a last resort.

    Of the three methods, homology modeling is the star. This is due, in part, to the current availability of a large number of experimentally determined protein structures. Although many tools and servers are available for homology modeling, the main steps you need to follow for these programs are almost the same.


    Industry leading IUPAC naming algorithms

    Accurate Language

    Our algorithms name molecules naturally and accurately, down to the character and formatting. If you find any problems, simply contact us with the structure so we can correct it.

    Broad Scope

    The entire history of the IUPAC nomenclature library is used in our development. The majority of the periodic table is handled.

    Customization

    Over 40 options for customizing how names are generated, or to switch between various IUPAC rules.

    Auto-updating Labels

    Display IUPAC names for your structures that automatically update as you draw them. You can even display IUPAC locants on your structures to help with descriptions.

    Name to Structure

    IUPAC names can be parsed into structure representations as well.


    3D Bones and Organs (Anatomy)

    3D Bones and Organs (Anatomy) is a free 3D anatomy app for Windows 10. It provides a dedicated 3D Anatomysection to study human body system. You can also explore individual systems like brain, muscles, skeleton, heart, organs, etc.

    In 3D Anatomysection, you can select systems including Muscular System, Circulatory System, Digestive System, Nervous System, Respiratory System, and Urogenital System. It lets you select male or female body to study human anatomy based on gender. You can easily rotate and zoom the view of a human structure using mouse. You can select a part and view its name and short information. It provides a feature to pronounce the name of a selected body part.

    It is a nice app to explore and study human anatomy in 3D. It also supports French and Spanish languages other than English. It contains a quiz feature too, but that didn’t work fine while my testing.


    Visualizing Structures with UCSF Chimera for Beginners

    Learn the basic functionality of UCSF Chimera, such as loading PDB coordinates into the software, manipulating the structure in 3D, and saving your session.

    Chimera Menus

    Review various functions in the UCSF Chimera Menus.

    Chimera Selections

    Learn how to select parts of a protein structure using UCSF Chimera.

    Chimera Structure Analysis

    Learn how to use some of the tools of UCSF Chimera to analyze and explore a protein structure.

    Chimera Structure Compare

    Learn how to compare the structures of two related proteins/domains and visualize the superposed structures of these proteins/domains.

    About PDB-101

    PDB-101 helps teachers, students, and the general public explore the 3D world of proteins and nucleic acids. Learning about their diverse shapes and functions helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy.

    Why PDB-101? Researchers around the globe make these 3D structures freely available at the Protein Data Bank (PDB) archive. PDB-101 builds introductory materials to help beginners get started in the subject ("101", as in an entry level course) as well as resources for extended learning.


    Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies

    The recent severe acute respiratory syndrome, known as Coronavirus Disease 2019 (COVID-19) has spread so much rapidly and severely to induce World Health Organization (WHO) to declare a state of emergency over the new coronavirus SARS-CoV-2 pandemic. While several countries have chosen the almost complete lock-down for slowing down SARS-CoV-2 spread, the scientific community is called to respond to the devastating outbreak by identifying new tools for diagnosis and treatment of the dangerous COVID-19. With this aim, we performed an in silico comparative modeling analysis, which allows gaining new insights into the main conformational changes occurring in the SARS-CoV-2 spike protein, at the level of the receptor-binding domain (RBD), along interactions with human cells angiotensin-converting enzyme 2 (ACE2) receptor, that favor human cell invasion. Furthermore, our analysis provides (1) an ideal pipeline to identify already characterized antibodies that might target SARS-CoV-2 spike RBD, aiming to prevent interactions with the human ACE2, and (2) instructions for building new possible neutralizing antibodies, according to chemical/physical space restraints and complementary determining regions (CDR) mutagenesis of the identified existing antibodies. The proposed antibodies show in silico high affinity for SARS-CoV-2 spike RBD and can be used as reference antibodies also for building new high-affinity antibodies against present and future coronaviruses able to invade human cells through interactions of their spike proteins with the human ACE2. More in general, our analysis provides indications for the set-up of the right biological molecular context for investigating spike RBD-ACE2 interactions for the development of new vaccines, diagnostic kits, and other treatments based on the targeting of SARS-CoV-2 spike protein.

    Keywords: ACE2 and ACE inhibitors COVID-19 Comparative modeling Coronavirus Fold recognition tools Neutralizing antibodies Receptor binding domain SARS-CoV-2 Spike Spike post-fusion conformation n-CoV19.

    Figures

    Extract of the MSA of SARS-CoV-2 spike protein monomer with the sequences of…

    SARS-CoV-2 spike protein (S-II domain)…

    SARS-CoV-2 spike protein (S-II domain) 3D model in post-fusion conformation. Lateral view (…

    SARS-CoV-2 spike protein regions involved…

    SARS-CoV-2 spike protein regions involved in the pre/post-fusion conformational transitions. Topology panel: schematic…

    SARS-CoV-2 spike protein regions involved…

    SARS-CoV-2 spike protein regions involved in the pre/post-fusion molecular packing. a , g…

    Multiple sequence alignment of RBDs…

    Multiple sequence alignment of RBDs from 11 SARS-CoV and 3 MERS-CoV strains. The…


    CATH / Gene3D v4.3

    3D Structure

    Find out what 3D structure your protein adopts

    Protein Evolution

    Learn about a particular protein family and how it evolved

    Protein Function

    Investigate the function of your protein

    Conserved Sites

    Look at protein sites that are highly conserved and implicated in function

    Download Data

    Download data files and query CATH via webservices

    Learn more

    Find out how CATH is created and maintained, how to link to CATH and more

    What is CATH-Gene3D?

    CATH is a classification of protein structures downloaded from the Protein Data Bank. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor.

    Gene3D uses the information in CATH to predict the locations of structural domains on millions of protein sequences available in public databases. This allows us to include additional annotations to the CATH-Gene3D database such as functional information and active site residues.

    If you have any questions, comments or suggestions please get in touch via Twitter, ask a question in our online forum or visit our support page.

    Latest Release Statistics Info

    CATH-Plus 4.3.0 CATH (daily snapshot)
    PDB Release 01-07-2019 25-06-2021
    Domains 500238 536769
    Superfamilies 5481 6631
    Annotated PDBs 150885 171886

    Gene3D v21
    Protein Sequences82,665,384
    CATH Domain Predictions151,013,797

    Citing this resource

    If you find the information in this resource useful, please consider using the following citations: