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
From Boltz-1 to Boltz-2: Did We Finally Bridge the Gap Between Structure and Affinity?
In modern biology, accurately simulating biomolecular interactions is a major difficulty. Our capacity to predict biomolecular complex structures has significantly improved with recent developments...
D-I-TASSER Outperforms AlphaFold? A New Frontier in Protein Structure Modeling
The requirement and utility of conventional force field-based folding simulations have been called into question by the overwhelming success of deep learning techniques in...
Unlocking Biomolecular Secrets with AF3Score: A Leap Forward in Structural Evaluation
Researchers from Changping Laboratory in Beijing introduced AF3Score, a novel adaptation of AlphaFold3 designed to evaluate biomolecular structures with unprecedented accuracy. This innovation addresses...
Overlapping Genes, Unfolding Insights: Synthetic Biology Meets AI
Given that the sharing of codon nucleotides dramatically reduces the size of protein sequences, viruses in nature often generate overlapping genes (OLG) in alternate...
PhysDock: A New Era in Protein-Ligand Docking with AI and Physics
In a breakthrough that could transform drug discovery, a team of researchers from ShanghaiTech University has introduced PhysDock, a novel AI-powered model designed to...