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
How D&D-seq Is Making Hard-to-Detect DNA-Protein Interactions Visible
If you've ever tried to figure out exactly where a transcription factor sits down on the genome inside a single cell, you know it's...
BioReason-Pro Allows Structured Reasoning for Protein Function Predictions
A team of scientists from the University Health Network - Canada's Hospital, Arc Institute and Vector Institute developed BioReason-Pro to tackle one of the...
PPIscreenML: A Rigorous Machine Learning Approach to Screening Protein-Protein Interactions with AF2
Every second, thousands of proteins inside your cells are bumping into each other, forming fleeting partnerships, and splitting apart again. These protein-protein interactions (PPIs)...
Meet FrustrAI-Seq: Proteome-Wide Frustration Profiling Without Structural Inputs
Proteins are remarkable molecules. They fold, bend, bind, and catalyze, all while balancing an internal tension that most biology textbooks barely mention. That tension...
Insilico Medicine’s PandaClaw: An Agentic AI for Therapeutic Discovery
For decades, the bottleneck in drug discovery wasn't the biology; it was the translation. Getting from a disease hypothesis to a viable therapeutic target...