15 Open-source Free Web-based 3D Molecular and Protein Modelling Software
- 1- LiteMol: 3D macromolecular. LiteMol is a 3D macromolecular renderer, It's built as a web & browser-based app, it...
- 2- ChemDoodle. The ChemDoodle Web Components library is an open source and free HTML5 toolkit for building scientific...
- 3- NGL Viewer: WebGL Viewer for Molecular Visualization.
Full Answer
Why choose our protein analysis software?
We offer the most accurate analysis of your data, quantifying species down to trace amounts. Our software is powered by unique algorithms that help researchers minimize ambiguity, achieve reproducibility, and eliminate lab-to-lab variability. We want protein researchers to enjoy their science, not be frustrated by their software.
What is the best software for protein-protein interaction prediction?
If your goal is just a surface analysis of the interaction, the UCSF Chimera is appropriate, but if your analysis contains details of the interaction , the BIOVIA Discovery Studio Visualizer is very useful. Is there any good protein protein interaction prediction software or tools?
What is proteinpilot software?
Combining sophisticated algorithms with an intuitive interface, you can now confidently identify more proteins and search large numbers of post translational modifications, without increasing search time or false positives. ProteinPilot Software is compatible with all proteomics MS/MS systems via the.*mgf format. Get to Know ProteinPilot Software >
What is pro group algorithm for protein-grouping analysis?
The embedded, industry-leading Pro Group Algorithm for protein-grouping analysis enables you to quickly and easily achieve protein isoform and protein subset differentiation, as well as false positives suppression. The unique user-interface is designed with biology in mind.
Which software is used for protein structure analysis?
MODELLER. MODELLER is a computer program for comparative protein structure modeling (http://salilab.org/modeller) (17,18).
How do you analyze proteins?
PROTEIN IDENTIFICATION There are two methods that are commonly used to identify proteins: Edman Degradation and Mass Spectrometry. Developed by Pehr Edman, Edman Degradation is a method of sequencing amino acids in a peptide.
What are bioinformatic tools?
Bioinformatics tools are software programs that are designed for extracting the meaningful information from the mass of molecular biology / biological databases & to carry out sequence or structural analysis.
What is Expasy used for?
It is an extensible and integrative portal which provides access to over 160 databases and software tools, developed by SIB Groups and supporting a range of life science and clinical research domains, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry.
What is the use of protein analysis?
A protein analyzer is a handy laboratory tool for determining the protein quantity in a sample. These instruments are most often found in food and beverage laboratories where they are used in assessment of nutritional content of meats, dairy products, and beyond.
Why do we do protein analysis?
Protein analysis is crucial to elucidating the function of proteins and understanding the impact of their presence, absence and alteration. This is key to advancing knowledge about diseases, providing the opportunity for biomarker discovery and development of therapeutics.
How can I learn bioinformatics?
How to Learn Bioinformatics: Step-by-StepLearn biology. Study the area of biology associated with the field of bioinformatics you are interested in. ... Study computer programming. Learn a programming language commonly used in bioinformatics. ... Choose a course. ... Study statistics. ... Start practicing bioinformatics.
What is the most important tool used in bioinformatics?
BLAST (Basic Local Alignment Search Tool) is one of the most widely used tools to gain sequence information.
What is Fasta and BLAST?
FASTA and BLAST are the software tools used in bioinformatics. Both BLAST and FASTA use a heuristic word method for fast pairwise sequence alignment. It works by finding short stretches of identical or nearly identical letters in two sequences. These short strings of characters are called words.
What is Swiss-Prot database?
SWISS-PROT (1) is an annotated protein sequence database, which was created at the Department of Medical Biochemistry of the University of Geneva and has been a collaborative effort of the Department and the European Molecular Biology Laboratory (EMBL), since 1987.
What is PubMed in bioinformatics?
PubMed is a free resource supporting the search and retrieval of biomedical and life sciences literature with the aim of improving health–both globally and personally. The PubMed database contains more than 34 million citations and abstracts of biomedical literature.
What is the Blast program?
BLAST is an acronym for Basic Local Alignment Search Tool and refers to a suite of programs used to generate alignments between a nucleotide or protein sequence, referred to as a “query” and nucleotide or protein sequences within a database, referred to as “subject” sequences.
All Answers (15)
For your issue, I believe you have to use machine learning solutions. For the PPI, Neural Networks (NNs) are a popular alternative, you can find several open source NNs toolboxes.
Similar questions and discussions
Is there any good protein protein interaction prediction software or tools?
What is WebGL?
Nowadays WebGL is a trending technology as it allows developers to create complex 3D interactive graphics, games using modern browsers as a client, without the need to install additional plugins, extensions, or software. WebGL allows the browser to work directly with the GPU (graphics processing unit).
WebGL for scientific and medical apps
It's a progressing technology, it's used now to create 3D web-based games, interactive 3D showcase, and simulations. It's also used in medicine, and we have covered the usage of WebGL in medical applications like Web-based DICOM apps like Med3Web, & Anatomy apps.
1- LiteMol: 3D macromolecular
LiteMol is a 3D macromolecular renderer, It's built as a web & browser-based app, it comes with a set of open source tools to build heavy-duty libraries and apps like 3D molecular data streaming, & 3D volumetric data streaming.
2- ChemDoodle
The ChemDoodle Web Components library is an open source and free HTML5 toolkit for building scientific WebGL applications. 2D components are also available, including chemical structures, sketchers, spectra, periodic tables, reactions and more!
3- NGL Viewer: WebGL Viewer for Molecular Visualization
NGL Viewer is a web application for molecular visualization. WebGL is employed to display molecules like proteins and DNA/RNA with a variety of representations. Src
4- GLMol
GLmol is an open source WebGL viewer project that allows developers and researchers to render interactive 3D molecular graphics and embed it in any webpage with ease. It's based on WebGL and JavaScript. GLmol displays biological assembly, displays unit cell, shows crystal packing and provides surface calculation and visualization.
5- Speck
Speck is an open source 3D molecule renderer aiming to produce attractive 3D figures.
One-stop stability
Cracking stability using a pile of one-trick, protein-hungry tools is a ton of work. Uncle combines 3 different measurement modes — fluorescence, Static Light Scattering (SLS) and Dynamic Light Scattering (DLS). So you can crank out all your data in just a few hours, and use way less protein.
Uncover way more in one shot
Trying new formulations or constructs? Get answers for up to 48 samples in under 2 hours. Measure T m and T agg at the same time and know when unfolding leads to aggregation. Add a DLS read before the temp ramp to know if you’ve got aggregate trouble right out of the gate.
AAV capsid stability
Uncle teams up with SYBR Gold to get a read on when your DNA starts to leak — way before the AAV capsid pops. Quantify initial free DNA and the amount that’s on the loose after a thermal ramp. Know when aggregation gets out of hand and tackle particle titer with SLS and DLS.
Unleash the Uni
Get more data with way less protein. The Uni only needs 9 μL of sample, and you pick how you use it. Run 1 sample in the morning, 48 in the afternoon. Do a DLS read if that’s all you need. Or, check DLS, then start a 3-day experiment to monitor real-time stability. Your samples are sealed airtight, so runs can be short or long — your call.
Full-spectrum
Biologics behave differently. With Uncle, you get the whole fluorescence spectrum, so you don’t need to know ahead of time how your protein behaves. If you want to try out some new tricks with dyes, Uncle can pick up on those too. Uncle catches aggregation with two wavelengths — so you’ll see it no matter what.
21CFRp11
If you’re working in regulated environments, you know that controlling access to data and keeping its integrity are a must-have. Uncle has 21CFRp11 compliant software tools that can be turned on without a hitch.