Research Tools

Automated protein structure homology modeling server

Deep learning system for protein structure prediction

GRAMM systematically maps the intermolecular energy landscape by predicting a spectrum of docking poses corresponding to stable (deep energy minima) and transient (shallow minima) protein interactions

Model reliability assessment for protein structures

The PSIPRED Workbench provides a range of protein structure prediction methods

a hierarchical approach to protein structure prediction and structure-based function annotation

An automatic protein docking server

an interactive tool for the exploration of macromolecular interfaces

Comparison and 3D alignment of protein structures and examination of a protein structure for similarity with the whole PDB archive or SCOP archive

This tool allows the selection of protein 3D structures for alignment

Fast and accurate protein structure search

An algorithm for sequence independent protein structure comparisons

The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB)

Using information fusion model to annotate enzyme catalytic active site

Compute various physical and chemical parameters for a given protein sequence

Protein hydrophobicity analysis and prediction

Predict the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria and Eukarya

Prediction of soluble protein expression in Escherichia coli

CAZypedia has been initiated as a community-driven resource to assemble a comprehensive encyclopedia of the "CAZymes," the carbohydrate-active enzymes and associated carbohydrate-binding modules involved in the synthesis and degradation of complex carbohydrates

DeepTMHMM is a deep learning protein language model-based algorithm that can detect and predict the topology of both alpha helical and beta barrels proteins over all domains of life

Antimicrobial peptide calculator and predictor

Protein Tool calculates isoelectric point and net charge of proteins, as well as the exact mass and the absorption coefficient using the amino acid sequence

This server predicts whether a protein is DNA-binding from its structure and/or sequence

HHpred is a method for sequence database searching and structure prediction that is as easy to use as BLAST or PSI-BLAST and that is at the same time much more sensitive in finding remote homologs

BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance

A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures

The MEME Suite allows you to discover novel motifs incollections of unaligned nucleotide or proteinsequences, and to perform a wide variety of other motifbased analyses

Dot matrix sequence comparison tool

Pairwise Sequence Alignment is used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid)

Multiple Sequence Alignment (MSA) is generally the alignment of three or more biological sequences (protein or nucleic acid) of similar length

BPROM is bacterial sigma70 promoter recognition program with about 80% accuracy and specificity. It is best used in regions immediately upstream from ORF start for improved gene and operon prediction in bacteria

NEBaseChanger assists in the design of primers for site-directed mutagenesis experiments using the Q5 Site-Directed Mutagenesis Kit

Try to find whether your sequence is similar to any annotated functional/defective IRES region

Tool for promoter search in prokaryotic genomes

a tool for locating promoters in phage genomes, using machine learning methods

The ViPTree server generates a "proteomic tree" of viral genome sequences based on genome-wide sequence similarities computed by tBLASTx

An expert system for genome assembly, annotation and visualization, featuring interactive circular and linear genome maps

Interactive Tree Of Life is an online tool for the display, annotation and management of phylogenetic and other trees. Manage and visualize your trees directly in the browser, and annotate them with various datasets.

Evolview allows users to upload, edit, annotate and share phylogenetic trees in various formats and styles.

PhageScope is an online bacteriophage database that offers comprehensive annotations, including completeness assessment, phenotype annotation, taxonomic annotation, structural annotation, functional annotation, and genome comparison.