Functional Protein Sequence Pattern Database
Different methods have been used in the developtment of FPSPD. Environment-dependent substitution tables and evolutionary trace analysis to identify those residues that can be considered involved in functional interactions. Solvent accessibility calculations to estimate the availability of particular residues and patterns to be directly involved in functional interactions. And, finally, knowledge of the three-dimensional structure to estimate the borders of the patterns.
The method yielded 3584 patterns, from 617 HOMSTRAD families, that are considered functional and 3049 that are probably functional. FPSPD Could be useful for assigning a protein to a homologous superfamily and thereby providing clues about function.
Structural validation by assessment of the Ramachandran plot
A fold recognition method using structural environment-specific substitution tables and structure-dependent gap penalties
A fully automated evolutionary trace server
The server takes a sequence alignment as the input and performs ET analysis. The resulting phylogenetic tree and the trace information are available in both JPEG and PostScript format. Any sequences with a PDB code as the sequence name will be regarded as known structures and the server will retrieve the PDB co-ordinates files and map the ET results onto each structure. Rasmol and Molscript input files for the mapping are provided for viewing and/or high-resolution printing.
Protein structure and alignment analysis
JOY takes an input alignment (or a single sequence) in a format similar to that of the NBRF/PIR format and produces a number of output files, including the annotated alignment in PostScript, LATEX and HTML. JOY requires a series of datafiles containing information about secondary structures, solvent accessibility and hydrogen bonding. These are produced automatically from a PDB file
Site Directed Mutator for predicting stability changes upon mutation
Systematic Annotation of Marcro molecULes
SAMUL is a web-based database system in which users can browse structural and functional annotations proteins at their residue level. The local structural environment (by the scheme of 64 environments) of amino acid residues can be determined by JOY and visualized in the context of three-dimensional structure with Jmol, a molecular viewer. For functional annotations, 26 UniProt feature annotations are utilized and the information is transferred onto their corresponding positions in terms of three-dimensional structures if available.
SAMUL also accommodates amino acid variations and mutations information so that users could browse and interprete them by looking their structural and functional environments at the same time.
Mapping Analogous Hetero-atoms onto Residue Interaction
MAHORI.org provides 3D visualization of fragment –residue interaction between the chemicals and multiple protein binding partners in the Protein Data Bank. In addition to providing the interaction type and the amount of bonds that the fragment made, it also shows the biochemical pathways affected by the chemical fragment via our chemical searching panels. A chemical fragment that affects different pathways in different organisms can open door for a more robust and insightful analysis for the study of species selectivity, off-target inhibition that causes drug side effect, and multi-target drug design.