Welcome to SAMUL

SAMUL is a web-based database system which enables users to browse structural/functional annotations of amino acid residues of proteins as macromolecules. The local structural environment (by the scheme of 64 environments64 environments) of amino acid residues could be determined by JOY and presented with a molecular viewer such as Jmol. For functional annotations, 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.

What SAMUL Provides

Sequence-Structure Mapping: We developed a method, double-map, which aligns a UniProt sequence to its corresponding PDB structure at residue level. Also, within a PDB file, sequence from SEQRES record and that of ATOM record has been aligned and presented. This enables to see which residues has been modified or failed to crystalized from the original sequence studied. [example]

Rich Annotations: By using double-map, UniProt annotations, especially feature (FT) records, can be harnessed and interpreted in 3D structures of proteins. In addition, nsSNPs that occur at protein coding regions could be mapped onto their corresponding amino acids in the context of 3D structure. [browse]

Gbrowse: Structure/function annotations are graphically visualized and highlighted at the reisude level of UniProt (or Ensembl) protein sequence by using Generic Genome Browser. [example]

Jmol: You can browse three-dimensional structure of a protein featuring structural/functional annotations within Jmol molecular viewer. [example]

DAS: SAMUL is a DAS (Distrubuted Annotation System) server, which provides a XML-based web service to distribute annotations through the web. [Database Source Name(DSN) of SAMUL] [example]