- 3D-PSSM Protein Fold Recognition Server
Method for Protein Fold Recognition using 1D and 3D Sequence Profiles coupled with Secondary Structure and Solvation Potential Information.
- Blocks Searcher
Compare a protein or DNA sequence to a database of protein blocks, retrieve blocks, create new blocks, and more.
- Bork Group WU-BLAST2 Search
- CBS Prediction Servers
Includes DictOGlyc and NetOGlyc (predition of O-glycosylation sites), SignalP (signal peptide) and TMHMM (transmembrane helices).
- ClustalW2 Multiple Sequence Alignment
- European Bioinformatics Institute Tools
A comprehensive range of tools for the field of bioinformatics.
- European Molecular Biology Laboratory (EMBL) Bioinformatics Services
A comprehensive Python-based system for macromolecular structure solution
A comprehensive Python-based system for macromolecular structure solution.
- PredictProtein Server
Sequence analysis, structure and function prediction.
- The Proteomics Center at Children's Hospital Boston
Searchable database of all core facilities within Children's Hospital and Harvard University. The cores are indexed by institution and by service category.
- PyMOL Molecular Viewer
Molecular viewer, render tool, and 3D molecular editor developed for visualization of 3D chemical structures, as well as small molecule structures.
- Python Programming Language
A programming language that lets you work more quickly and integrate your systems more effectively.
Full-chain protein structure prediction server
- Rosetta Commons
The Commons provides an environment for continuous sharing and collaborative development of the Rosetta software platform.
- Rosetta Design
Identifies low energy sequences for specified protein backbones, and has been used previously to stabilize proteins and create new protein structures.
Sequence analysis; architecture analysis; domain searching and browsing; HMMs.
Contains links to a large array of prediction tools and analytical software.
- UCLA-DOE Institute for Genomics and Proteomics
- American Crystallographic Association (ACA)
- Argonne Guest House: Reservations
- Argonne National Laboratory
- Cryopreservation Wiki
- Dundee PRODRG2 Server
- Electron Microscopy for Dummies
- Hampton Research Technical Support
- International Union of Crystallography (IUCr)
- miniTweezers Lab
- Protein Structure Initiative (PSI)
Aims at determination of the 3D structure of all proteins
- Rosetta Dock Server
- Structural Medicine at Cambridge University (Randy Read)
- Dana-Farber/Harvard Cancer Center(DFCI/HCC)
- DFCI Core Facilities
Mass Spec, DNA/Protein Sequencing, Peptide Synthesis
- DFCI/HCC DNA Sequencing Core
- Harvard Microchemistry and Proteomics Analysis Facility
Mass Spec, Protein sequencing, Proteolytic and Chemical Cleavage of Proteins, Microcapillary and Microbore rpHPLC, Amino Acid Analysis.
- HMS Biopolymers Facility
- HMS Core Facilities
- HMS Research Computing Group
- IDI Core Facilities
- Proteomics Center at Children's Hospital Boston
Mass spec, protein analysis.
- Biological Macromolecule Crystallization Database (BMCD)
A hierarchical domain classification of protein structures by class, architecture, topology (fold family), and homologous superfamily
- Dali Server
Network service for comparing protein structures in 3D
- Database of Macromolecular Movements
Molecular motion classifications and movies
- Entrez Protein Database
- ExPASy Proteomics Server
Links to ProtParam, Peptide Cutter, PSIpred. Analysis of protein sequences, structures, and 2D PAGE; links to databases, proteomics tools and software packages, molecular biology resources.
- Heavy Atom Databank
- HLDA Antibody Database
Leukocyte workshop antibody and CD nomenclature
- HOMSTRAD: Homologous Structure Alignment Database
- Human Gene Mutation Database (HGMD)
- Immunological Genome Project
- Knockout Mouse Project (KOMP) - UC Davis
- NCBI BLAST
- NIH RePORT
A database of biomedical research funded by the NIH
A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models(HMMs)
PRINTS is a compendium of protein fingerprints.
- ProDom (Protein Domain Database)
Automatic compilation of homologous domains; analyze domain arrangements of proteins and protein families
Sites, patterns and profiles; various access and search tools; documentations; and more
- Protein Data Bank (PDB)
Information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. Biomolecular structure database; SearchFields; links to macromolecular structure related resources; and more
Search literature, Protein, Nucleotide, Genome, PopSet, OMIM, Taxonomy, Books, ProbeSet, and 3D Domains.
Structural classification of proteins by class, fold, superfamily, family, protein, and species.
Database of structural and functional annotation for all proteins and genomes
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
- VWF Database
University of Sheffield ISTH-SSC VWF Online Database
- WTSI Mouse Resources Portal (Sanger)
Unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute's primary screen.
- Countway Library of Medicine (HMS)
- eCommons of Harvard Medical School
- Harvard Immunology Seminar Series
- HMS Events Calendar
- HMS White Pages
- HMS Tech Services
- IDI File Transfer Portal
- PhD Poster Affiliation Logos
- Program in Cellular and Molecular Medicine
- Whitehead Institute Events Calendar
- Cell Migration Gateway
The Cell Migration Gateway is a comprehensive and regularly updated resource for anyone interested in cell migration.
- Cold Spring Harbor Protocols
- Current Protocols in Immunology: Wiley InterScience
- Encyclopedia of Actin-Binding Proteins
Non-exclusive A to Z of actin-binding proteins and has been compiled in an attempt to bring create some semblance of order to the rapidly increasing list.
- Inflammation: The Leukocyte Adhesion Cascade
Mechanisms, processes, cells and molecules involved in inflammation.
- Medical Histology Index
- Molecular Biology Gateway
Information and links on molecular biology.
- NEB Restriction Endonuclease Index
- Platelet-Type von Willebrand Disease Blog (PT-VWD)
- Therapeutic Immunology Group (TIG)
Monoclonal Ab info, research labs, articles and protocols.
- Biocompare for Life Scientists
Search lab products and reagents and compare for best pricing.
- BioMath Calculator
DNA & Temperature Conversions and Conversion Factors for Molecular Biology
- Centrifuge Rotor Calculator
- Fluorescence SpectraViewer
Plot and compare spectra and check compatibility.
- Hampton Research Crystal Optimization Calculator
- IDT Custom Oligo Ordering
- Ligation Calculator
- OpenWetWare Information Sharing for Researchers
- PE conjugation of antibodies
- Protein Calculator
- Radioactive Decay Calculator
- Reverse Complement Tool
- Sigma Buffer Calculator
- TeraGrid User Portal
- TeX Catalogue
- Unit Converter
Macromolecular crystallography software.
- Barton Group Software
Access to STAMP (Structual Alignment of Multiple Proteins), ALSCRIPT (Sequence alignment to PostScript) and DOMAK (DOMain Maker).
Macromolecular crystallography software.
Crystallography and NMR system software.
Nonlinear regression resource for analysis of biological data.
- Debian GNU/Linux
- DNAStrider 1.59.2
Sequence analysis software, free download.
- Free Molecular Visualization Software
A comprehensive list of links to softwares available.
- Free Software Foundation
- GCG Web Interface
Tools for protein and DNA/RNA analysis.
Molecular visualization and analysis.
X-Ray Crystallography software.
Profile hidden Markov models for sequence analysis.
- HMS Software Downloads
- Lasergene (DNASTAR)
Sequence analysis software, download for Mac OS X or Windows.
- MEME Suite
Discovers motifs in groups of related DNA or protein sequences.
Homology or comparative modeling of protein 3D structures.
Molecular Graphics software: displaying, analyzing and manipulating 3D structures.
- NIH Imaging Analysis Software
Programs for inferring phylogenies.
- Sanger Institute Software Downloads
Production sequencing, physical mapping, informatics analysis software.
- Sequence Alignment and Modeling System (SAM)
Create, refine and use hidden Markov models for sequence analysis.
- Situs Download
SOLVE: Automated crystallographic structure solution for MIR, SAD, and MAD.
RESOLVE: Statistical density modification, local pattern matching, automated model-building, automated ligand-fitting, and prime-and-switch minimum bias phasing.
SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy.
- Structural Biology Software Database
- Twinning Server
- Uppsala Software
Software and Resources for Macromolecular Crystallography and Structural Biology.
- WHAT IF
Versatile molecular modeling package that is specialized on working with proteins and the molecules in their environment.