Here is a listing of a variety of online tools and resources that are available that greatly enhance your knowledge of the structure of biological macromolecules. As we are well aware, the structure of a protein determines its function. Therefore, the study of how proteins work depends on an in-depth knowledge of the structure of said protein. The websites listed here are sites that I have found to be very useful in enhancing knowledge of protein structure. The sites listed on this page are not commercially endorsed by either myself or Tennessee Technological University, and I am not receiving any form of compensation for listing them here. This list serves the purpose of providing users with easily-accessible links to use these packages and learn more about how they are used and applied, and many of them will be used by the tutorials featured on this site.
Click on the link in the heading below of each online software package to access the website.
ClusPro
The ClusPro web server is a useful tool for protein-protein docking. ClusPro accepts two PDB files of proteins as input, and performs rigid body docking calculations, scoring the best possible docks by clustering similar docked conformations into several cluster centers. The web server is customizable with a variety of advanced options, and relatively easy to use.
Evolutionary Trace
The Evolutionary Trace server provides information on the structure and function of proteins by enhancing the tools available in the widely used BLAST search & alignment methods. Evolutionary Trace goes a step further by computing the relative rank of functional structural importance among many homologous proteins in many species. The rank is lower if the sequence positions in homologous proteins are evolutionarily-related, and the rank is higher if the species are evolutionarily-divergent. This tool is very useful when combined with a tool such as the Protein Frustratometer in identifying key parts of a protein and identifying things like the active site.
Protein Data Bank
The Protein Data Bank (PDB) is the primary repository of known protein 3D structures, with over 200,000 structures that have been experimentally-determined by X-ray Crystallography, NMR, or other methods, such as cryo-electron microscopy. The database is searchable and all structures may be downloaded free of charge and imported into most viewing software such as Chimera X or MOE. Structures in the database may also be accessed via the UniProt database, or directly from within viewing software by the PDB accession code, a unique four-letter alphanumeric code that identifies the structure in question.
Protein Frustratometer
The Protein Frustratometer is an algorithm based on Energy Landscape Theory that quantifies the magnitude of local frustration exhibited by specific amino acid residues. During the process of folding, the protein follows a rugged, funnel-shaped energy diagram, As protein contacts are formed, the protein falls lower and lower in the funnel and ultimately arrives at its native conformational state, which is accepted as the protein’s structure. Yet the rugged nature of this funnel means that there are many local minima, and many of these are tied to higher energy states of specific amino acid residues. These higher energy states may be a result of the fact that the protein is not finished at that part — it still needs to “do something” there. So these highly-frustrated residues may be sites of protein-protein or ligand interactions. As such, this tools is very useful for predicting these potential interactions in biomolecules.
UniProt Database
UniProt is a comprehensive database of protein structure knowledge and information. This database consists of the primary structure information (sequence) of over 350 million proteins in a wide variety of known species. There is also information in UniProt of the names & taxonomy, subcellular location, disease state, expression, protein interactions, and secondary structure information. UniProt also connects to the Protein Data Bank (PDB) for downloading structural information. The primary structure, FASTA files are simple text files containing the single-letter amino acid codes of the amino acids present, and are readable by many protein structure viewing programs, such as Chimera X or MOE. UniProt also provides access to BLAST search and alignment tools, which are very useful at identifying highly-conserved amino acid residues in protein that may be related to function.