The items shortlisted under the categories below are essential online tools designed to help researchers extract meaningful insights from the vast and complex data stored in molecular biology and biological databases. These tools are invaluable for carrying out sequence analysis, structural analysis, and other critical bioinformatics tasks, enabling scientists to explore, compare, and interpret biological sequences, structures, and functions efficiently. By leveraging these advanced bioinformatics tools, researchers can make informed decisions, accelerate their studies, and unlock new possibilities in the fields of genomics, proteomics, and beyond.
Bioinformatics databases are repositories that store biological data, such as nucleotide sequences, protein structures, and gene expression profiles. These databases are essential for researchers to access, retrieve, and analyze large datasets, enabling them to make significant discoveries in molecular biology and genetics.
NCBI
A comprehensive resource for biomedical and genomic information, including PubMed, GenBank, and many other databases.
European Nucleotide Archive - ENA Browser
A repository that provides access to comprehensive and freely available nucleotide sequence data.
EMBL-EBI
European Bioinformatics Institute offers freely available biological data and bioinformatics services for researchers.
DDBJ
The DNA Data Bank of Japan is a public repository for nucleotide sequences and associated biological information.
PlasmoDB
A database dedicated to the genomics of the malaria parasite Plasmodium, providing tools for data analysis and visualization.
GISAID
A global initiative providing open access to genomic data of influenza viruses and the coronavirus responsible for COVID-19.
VEuPathDB
An integrated database for eukaryotic pathogens, supporting research on various parasitic diseases.
HBVdb
A specialized database focused on the Hepatitis B virus, offering resources for the study of HBV genetics.
Virus Pathogen Database and Analysis Resource (ViPR
A database and analysis resource for viral pathogens, facilitating research on viral genomics, epidemiology, and more.
Drug design tools in bioinformatics facilitate the discovery and optimization of therapeutic compounds. These tools allow researchers to model and predict interactions between potential drugs and biological targets, accelerating the development of new medicines through computational approaches such as molecular docking, virtual screening, and pharmacophore modeling.
HADDOCK Web Server
A web server for docking small molecules, nucleic acids, and proteins using an integrative modeling platform.
Cluspro 2.0
A web server for protein-protein docking, providing fast and automated solutions for molecular docking problems.
HDOCK Server
An integrated protein-protein and protein-DNA docking server based on a hybrid algorithm.
Eukaryotes bioinformatics focuses on tools and resources for analyzing the complex genomes and proteomes of eukaryotic organisms. These tools help researchers investigate gene expression, protein interactions, and evolutionary relationships in organisms ranging from single-celled protozoa to multicellular plants and animals.
VEuPathDB
An integrated bioinformatics platform that supports research on eukaryotic pathogens by providing access to data and tools.
Galaxy
Galaxy is an open, web-based platform for data-intensive biomedical research. It provides a comprehensive suite of tools and workflows for analyzing large datasets, enabling users to create, share, and reproduce complex bioinformatics analyses without requiring programming skills.
PATRIC
The Pathosystems Resource Integration Center offers data and tools for bacterial infectious disease research.
EggNOG
A database of orthologous groups of genes, facilitating evolutionary and functional analysis of genomes.
RAPT - NCBI
NCBI's Rapid Annotation Tool for microbial genomes, providing automatic annotation of assembled genomes.
KEGG: Kyoto Encyclopedia of Genes and Genomes
A resource for understanding high-level functions of biological systems, linking genomic and molecular information with chemical and systemic information.
Genomics tools are designed to analyze entire genomes, enabling researchers to study the structure, function, and evolution of genes across different organisms. These tools help in identifying genetic variations, understanding gene regulation, and exploring the genetic basis of diseases.
PathogenFinder
A tool for predicting pathogenic bacteria based on their genome sequences, enabling faster identification of pathogens.
ResFinder
A tool for identifying antimicrobial resistance genes in bacterial genomes, supporting genomic surveillance.
KmerResistance
A tool for detecting resistance genes in bacterial genomes using k-mer-based approaches, supporting antimicrobial resistance research.
CARD
The Comprehensive Antibiotic Resistance Database provides a collection of curated reference sequences and computational models to detect resistance genes.
PubMLST
A database for multilocus sequence typing, providing a platform for the analysis of bacterial and fungal population genetics.
MLST
A web tool for performing multilocus sequence typing of bacterial isolates, aiding in the characterization of microbial populations.
VirulenceFinder
A tool for detecting virulence genes in bacterial whole genome sequences, supporting research on pathogenicity.
RAPT - NCBI
A tool from NCBI for rapid annotation of microbial genomes, providing functional and structural annotations.
KEGG: Kyoto Encyclopedia of Genes and Genomes
A knowledge base for linking genomic information with higher-level functional information, widely used for pathway mapping and systems biology.
MAFFT - a multiple sequence alignment program
A software for multiple sequence alignment, allowing efficient and accurate alignment of nucleotide and protein sequences.
iTOL
An online tool for the visualization, annotation, and management of phylogenetic trees, supporting large datasets.
Codon Usage Database
A database of codon usage tables for various organisms, aiding research on gene expression and protein synthesis.
Immunoinformatics tools focus on the computational analysis of the immune system. These tools are used to predict immune responses, design vaccines, and study interactions between antigens and antibodies. They are essential in advancing research in immunology, allergy, and vaccine development.
NetCTL
NetCTL is a computational tool used for predicting CTL (Cytotoxic T Lymphocyte) epitopes in proteins. It combines peptide binding predictions to MHC class I molecules, proteasomal C-terminal cleavage, and TAP transport efficiency to predict the most probable CTL epitopes.
BCpred server
BCpred is a computational tool that predicts linear B-cell epitopes with a focus on enhancing the prediction accuracy using machine learning techniques.
IEDB
IEDB (Immune Epitope Database) is a comprehensive resource that contains experimentally validated and predicted immune epitopes, helping researchers explore epitopes involved in immune responses.
VaxiJen
VaxiJen is an antigen prediction tool that classifies proteins as probable antigens or non-antigens, facilitating vaccine design without relying on sequence alignment.
BCEPRED Submission page
BCEPRED is a tool for predicting linear B-cell epitopes in protein sequences using various physicochemical properties like flexibility, hydrophilicity, and surface accessibility.
Scratch Protein Predictor
Scratch Protein Predictor is a suite of bioinformatics tools for predicting various structural and functional properties of proteins, including secondary structure, solvent accessibility, and disordered regions.
ExPASy - ProtParam tool
ProtParam is a tool on the ExPASy server that calculates the physicochemical parameters of a protein sequence, such as molecular weight, isoelectric point, and extinction coefficient.
ProSA-web - Protein Structure Analysis
ProSA-web is a tool that analyzes and validates protein structures by identifying erroneous parts in three-dimensional models. It is widely used in protein structure prediction and modeling.
Galaxy Refine
Galaxy Refine is a tool designed to improve protein models by refining their structure, using various energy minimization and molecular dynamics-based techniques.
AllerTOP
AllerTOP is a tool designed for the in silico prediction of allergens. It classifies proteins as allergens or non-allergens, aiding in allergenicity assessment during drug and food development.
ElliPro: Antibody Epitope Prediction
ElliPro is a web-based tool that predicts antibody epitopes based on the 3D structure of a protein. It combines geometrical properties to determine epitopes with high accuracy.
iMODS
iMODS is an online tool for normal mode analysis and simulation of molecular dynamics. It allows users to study the flexibility and large-scale motions of protein structures.
C-ImmSim
C-ImmSim is an immune simulation tool that mimics the immune response to an antigen. It is widely used in vaccine research and immunology studies to predict immune dynamics and outcomes.
NPS@ : SOPMA secondary structure prediction
SOPMA (Self-Optimized Prediction Method with Alignment) is a tool that predicts the secondary structure of proteins using multiple sequence alignments and optimized algorithms.
iBCE-EL
iBCE-EL is a computational tool used for predicting linear B-cell epitopes. It enhances the prediction accuracy by combining machine learning and biological data.
Sequence analysis tools allow researchers to analyze DNA, RNA, and protein sequences. These tools are crucial for tasks such as sequence alignment, motif discovery, and evolutionary analysis, helping scientists to uncover functional and structural insights from biological sequences.
Joint Interactive Nucleotide Analysis-Helix (JINA-H)
The Sequence Manipulation Suite offers a collection of tools for manipulating and analyzing DNA, RNA, and protein sequences. It includes functionalities for sequence alignment, translation, and secondary structure prediction.
The Sequence Manipulation Suite
The Sequence Manipulation Suite provides a range of tools for analyzing and manipulating DNA, RNA, and protein sequences. It offers functionalities for sequence alignment, translation, and secondary structure prediction, facilitating various bioinformatics analyses.
Expasy
Expasy is a bioinformatics resource portal that provides access to various tools and databases for protein and nucleotide sequence analysis, including protein structure and function prediction.
Metagenomics tools are designed to analyze genetic material recovered directly from environmental samples. These tools enable researchers to study microbial communities, identify species, and understand the functional diversity of microorganisms in various ecosystems, without the need for culturing individual species.
KmerFinder
KmerFinder is a tool used for identifying and analyzing k-mers (short sequences of nucleotides) in metagenomic data. It helps in the detection and characterization of microbial genomes.
Galaxy
Galaxy is an open, web-based platform for data-intensive biomedical research. It provides a comprehensive suite of tools and workflows for analyzing large datasets, enabling users to create, share, and reproduce complex bioinformatics analyses without requiring programming skills.
kbase
KBase is a platform for systems biology and bioinformatics research. It provides tools for analyzing and modeling biological data, including metagenomic and genomic datasets.
Next Generation Sequencing (NGS) tools provide powerful methods for analyzing high-throughput sequencing data. These tools help researchers process, align, and interpret large volumes of sequence data, enabling applications in genomics, transcriptomics, and personalized medicine.
UCSC Genome Browser Gateway
The UCSC Genome Browser Gateway provides access to the UCSC Genome Browser, a tool for visualizing and analyzing genomic data. It supports a wide range of genomic annotations and tools for data exploration.
PATRIC
PATRIC (Pathosystems Resource Integration Center) offers a comprehensive resource for bacterial genomes and associated data. It includes tools for genomic analysis, comparative genomics, and functional annotation.
Galaxy
Galaxy is an open, web-based platform for data-intensive biomedical research. It provides a comprehensive suite of tools and workflows for analyzing large datasets, enabling users to create, share, and reproduce complex bioinformatics analyses without requiring programming skills.
Structural biology tools are used to analyze and visualize the three-dimensional structures of biological macromolecules, such as proteins and nucleic acids. These tools enable researchers to understand the molecular architecture, function, and interactions of these structures, which is vital for drug design and functional biology studies.
SWISS-MODEL Interactive Workspace
SWISS-MODEL provides an interactive workspace for protein structure modeling. Users can build and refine 3D models of proteins based on homologous sequences and structural templates.
I-TASSER server for protein structure and function prediction
I-TASSER is a server for predicting protein structure and function based on homology modeling and ab initio structure prediction. It provides high-accuracy models for proteins with unknown structures.
PHYRE2 Protein Fold Recognition Server
PHYRE2 is a server for protein fold recognition and structural modeling. It helps in predicting the 3D structure of proteins based on sequence information and known protein structures.
Scratch Protein Predictor
Scratch Protein Predictor is a tool for predicting various aspects of protein structure and function. It provides methods for secondary structure prediction, protein disorder prediction, and other features crucial for understanding protein function and stability.
RCSB PDB
RCSB PDB is a database of protein and nucleic acid structures. It provides detailed information on the 3D structures of biological macromolecules and tools for visualizing and analyzing these structures.
ipynb - Colaboratory
Colaboratory (Colab) is a Google tool for running Python code in the cloud. The provided link offers a notebook for using AlphaFold2, a tool for protein structure prediction.
Viral bioinformatics tools are specialized for studying the genomes and proteomes of viruses. These tools help researchers analyze viral sequences, understand virus-host interactions, and track viral evolution. They are essential in epidemiology, vaccine design, and the development of antiviral therapies.
HBVdb
HBVdb is a database focused on hepatitis B virus (HBV) data, including genome sequences, genotypes, and associated clinical information. It supports research on HBV biology and treatment.
Virus Pathogen Database and Analysis Resource (ViPR)
ViPR is a database and analysis resource for viral pathogens. It provides tools for analyzing viral genomes, studying virus-host interactions, and understanding viral evolution.
GISAID
GISAID (Global Initiative on Sharing All Influenza Data) is a platform for sharing influenza and SARS-CoV-2 genomic data. It supports global surveillance and research on viral pathogens.
Galaxy
Galaxy is an open, web-based platform for data-intensive biomedical research. It provides a comprehensive suite of tools and workflows for analyzing large datasets, enabling users to create, share, and reproduce complex bioinformatics analyses without requiring programming skills.
PATRIC
PATRIC (Pathosystems Resource Integration Center) offers a comprehensive resource for bacterial genomes and associated data. It includes tools for genomic analysis, comparative genomics, and functional annotation.
EggNOG
EggNOG is a database for orthologous groups of proteins and functional annotations. It aids in functional annotation of genes and provides insights into evolutionary relationships between proteins.