Tag: iCn3D

Explore 3D Molecular Structures with iCn3D

Do you want to analyze three-dimensional structures and highlight important features like active site residues, point mutations, and binding partners? Check out NCBI’s “I see in 3D” (iCn3D) – a free, web-based tool that allows you to explore the structure of a biomolecule at an atomistic level.

Features & Benefits

Interactively view 3D structure and corresponding sequence data
Align a protein sequence with unknown structure to a sequence-similar 3D structure
Interactively view 3D alignments of similar structures
View the interaction interfaces in a structure
Save your custom display as a short URL or PNG image
Share a link to your customized display of a structure
Incorporate iCn3D into your own pages

Continue reading “Explore 3D Molecular Structures with iCn3D” →

Viewing Ligand-Protein Interactions in iCn3D

Are you interested in viewing how a protein interacts with a ligand? iCn3D, our 3D molecular structure viewer, now offers improved displays of these interactions at an atomic level.

Check out this example:

You are now able to see the interactions of an embedded ligand (such as the drug Gleevec in the protein ABL2) within iCn3D. In the image below, the left panel shows Gleevec colored by atom type and the interacting ABL2 protein residues colored in magenta. The right panel displays Gleevec as a 2D structure with interacting protein residues shown as magenta rectangles. In both panels, the dashed lines represent individual interactions, color-coded by interaction type as explained in the “Color Legend.” Hovering over a dashed lines will display the interaction type and length. Continue reading “Viewing Ligand-Protein Interactions in iCn3D” →

Universal Reference Numbers for Ig Domains Now Available in NCBI’s iCn3D Structure Viewer

The Immunoglobulin (Ig) fold is the most common protein structure unit in the human proteome and is involved in many cellular signaling pathways. NCBI along with researchers at the National Cancer Institute and California State University, Northridge have developed a universal reference numbering scheme for Ig folds, now available in the iCn3D structure viewer, to help you compare and analyze proteins with this common fold. iCn3D can also automatically detect Ig domains in structures by comparing them to a library of diverse Ig template structures. Continue reading “Universal Reference Numbers for Ig Domains Now Available in NCBI’s iCn3D Structure Viewer” →

Using NCBI Data and Tools for Your Research Project

Are you a biology student working on a research project? NCBI offers free access to a wide variety of resources and tools to help you find and download data for your project. 

How and why do you use our resources? Check out the example below:

Your professor has assigned you a research project looking at the sequence and structure of the TP53 gene in the domestic cat (Felis catus). In addition, you were asked to find information on this gene and its genomic region in other members of the cat family (Felidae). Continue reading “Using NCBI Data and Tools for Your Research Project” →

A Successful Codeathon! Collaborating to Expand Expertise in African Life Scientists

Exciting update! We recently collaborated with the African Society for Bioinformatics and Computational Biology (ASBCB) for their spring OMICS Codeathon, and it was a great success. ASBCB is a professional association dedicated to the advancement of bioinformatics and computational biology in Africa. Codeathons are events focused on technology and software development, where participants work collaboratively to solve problems.

The ASBCB codeathon program serves as a grassroots training initiative for expanding expertise among African life scientists. It aims to equip participants with valuable skills and knowledge in life science and biotechnology by using research projects, public datasets, and peer-to-peer learning. Continue reading “A Successful Codeathon! Collaborating to Expand Expertise in African Life Scientists” →

Navigating Between BLAST and iCn3D

Explore protein structures and sequences quickly and easily

Have you ever come across an unfamiliar protein in your BLAST results? With the newly added ‘AlphaFold Structure’ link (Figure 1), you can now explore its structure as predicted by AlphaFold in iCn3D. The iCn3D Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool with interactive displays of 3D structure, 2D topology, 1D sequence and annotation.

Features & Benefits

Upload AlphaFold structures to iCn3D directly
Use the structure search feature to find structures of interest
Understand important features of the structures, such as disease-associated variations (ClinVar), genetic variations (dbSNP), or chemical modifications (PTM)
Identify similarities and differences between AlphaFold predictions and experimentally determined structure
Gain insights into the structural characteristics and properties of the molecules
Use iCn3D in different platforms (Jupyter Notebook, Virtual Reality, and Augmented Reality)
Easily integrate iCn3D using scripted workflows (node.js, python) to analyze large sets of structures

Continue reading “Navigating Between BLAST and iCn3D” →

New Upcoming NCBI Virtual Workshops!

Apply to attend October 2022 interactive, hands-on workshops

Want to learn more about NCBI resources and how to implement our cutting-edge tools in your research? NCBI offers a variety of educational opportunities, including workshops, webinars, codeathons, tutorials, and more!

We are excited to announce our upcoming virtual workshop series for October 2022. Our interactive, hands-on workshops are taught by experienced NCBI Education Faculty. Applications are open to the public; however, each workshop will accept a limited number of participants to facilitate the best possible educational experience. Continue reading “New Upcoming NCBI Virtual Workshops!” →

Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022

Come visit NCBI at the Bioinformatics Open Science Conference (BOSC), part of the Intelligent Systems for Molecular Biology Conference (ISMB), July 13-16, taking place both in person in Madison, Wisconsin and virtually! We’ll be presenting talks and posters on the latest updates to the NCBI Datasets, BLAST, and Protein resources. You can also join us at the Birds of a Feather (BoF) discussion and the BOSC CollaborationFest (CoFest) to explore these resources and discuss workflows with NCBI staff. Continue reading “Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022” →

Structure viewer iCn3D version 3 featuring analysis of 3D structures!

The NCBI structure viewer iCn3D version 3 is now available on the NCBI web site and from GitHub.

Analysis of 3D Structures

You can use the current version with the icn3d package at npm to write scripts to call functions in iCn3D. For example, this script on GitHub can calculate the change in interactions due to a mutation. The results of this analysis for the structure (6M0J) of the SARS-CoV-2 spike protein bound to the ACE2 receptor are displayed in Figure 1. These show the predicted changes in interactions with other residues in the the SARS-CoV-2 spike protein and in the ACE2 receptor when the asparagine (N) at position 501 of the spike protein is changed to a tyrosine (Y). You can also run these scripts from the command line to process a list of 3D structures to get and analyze annotations.

Figure 1. iCn3D viewer showing the predicted interactions with other residues in the spike protein and in the ACE2 target when the asparagine (N) at position 501 of the SARS-CoV-2 spike protein is substituted with tyrosine (Y), highlighted in yellow. Interactions were calculated using the script interactions2.js.

Continue reading “Structure viewer iCn3D version 3 featuring analysis of 3D structures!” →

Structure viewer iCn3D 2.20.0 is available with new features including viewing an electrostatic potential map!

The NCBI structure viewer iCn3D 2.20.0 is now available on the NCBI web site and from GitHub. You can now view the electrostatic potential map for any subset of 3D structures within 30,000 atoms. The potential is calculated using the DelPhi program by solving a linear Poisson-Boltzmann equation. You can show the potential on a surface or show a equipotential map. The potential map shows the effect of charges on molecular interactions qualitatively.

The example in Figure 1 below shows the electrostatic potential for the binding of Gleevec to the human Abl2 protein. This new feature can be accessed from the menu “Analysis > DelPhi Potential.” You can also download the PQR file format with assigned partial charges.

Figure 1: 3GVU: The crystal structure of human ABL2 in complex with GLEEVEC. The ligand shows the -25 mV (red) and +25 mV (blue) equipotential map with a grid size 65, salt concentration 0.15 M, and pH 7. The protein shows the surface potential with a gradient from -75 mV (red) to +75 mV (blue).

Continue reading “Structure viewer iCn3D 2.20.0 is available with new features including viewing an electrostatic potential map!” →