BIOINFORMATICS TOOLS
Proteomics Tools
Protein Sequence Analysis and Function Prediction
- ProtParam – Allows the computation of various physical and chemical parameters for a given protein sequence.
- PEAKS CMD – It can perform de novo sequencing, protein identification, multi-engine protein identification,
PTM search, sequence homology searching and quantification. -
PEAKS Studio Xpro – A software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post-translational modifications (PTMs) and sequence variants (mutations), and peptide/protein de novo sequencing. (Commercial)
- PANTHER-PSEP – Estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein.
- ProtScale – It can compute and represent the profile produced by any amino acid scale on a selected protein.
- PredictProtein – Service for protein structure prediction, protein sequence analysis, protein function prediction, protein sequence alignments, bioinformatics.
- MutationTaster – Identifies disease-causing ability of sequence alterations.
-
MuPIT Interactive – Mapping variant positions to annotated, interactive 3D structures.
-
LS-SNP – An annotated database of SNPs. Currently only coding non-synonomous SNPs found in human genes are included.
- PeCop – Predicting Persistently Conserved Positions.
Protein Domain Prediction
- SMART@EMBL – The web server is used for the identification and analysis of protein domains within protein sequences..
- MEME – Motif-based sequence analysis tools.
- InterPro@EBI – Protein domain and family classification database.
- TMHMM 2.0 – Web server for the prediction of transmembrane helices in proteins.
Must Read
Unleash the Power of PPI3D: A Comprehensive Web Server to Explore, Analyze, and Model...
Understanding molecular mechanisms requires an understanding of protein interactions with nucleic acids. Researchers can query preprocessed and clustered structural data, analyze the data, and...
Untangling the Cellular Family Tree: GEMLI Estimates Lineage from scRNA-seq Data
Researchers from the Institute of Bioengineering, Lausanne, Switzerland, introduce GEMLI, a powerful computational tool that enables robust identification of cell lineages solely from scRNA-seq...
Smart Sampling for Smarter Drugs: How Active Learning Boosts Drug Discovery
In computational drug discovery, active learning (AL) is a potent approach that makes it possible to identify the best binders from large chemical libraries....
UC Berkeley’s Breakthrough RNA Language Models Predict Mutations that Enhance RNA Function
A new tool from UC Berkeley can predict mutations that can improve the way how RNA works. By leveraging hyperthermophilic RNAs, the researchers identified...
Supercharge Epigenomic Workflows with EAP: A Cloud-Based Platform for Comprehensive and Interactive Analysis of Large ChIP/ATAC-seq...
The significance of comprehending gene expression regulation in tissue development is highlighted by the examination of disease progression through methods such as ChIP-seq and...