ProteinDBS v2.0: a web server for global and local protein structure search

Abstract

ProteinDBS v2.0 is a web server designed for efficient and accurate comparisons and searches of structurally similar proteins from a large-scale database. It provides two comparison methods, global-to-global and local-to-local, to facilitate the searches of protein structures or substructures. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a high-running speed while preserving reasonably high precision of structural comparison. The experimental results show that our system is able to return results of global comparisons in seconds from a complete Protein Data Bank (PDB) database of 152 959 protein chains and that it takes much less time to complete local comparisons from a non-redundant database of 3276 proteins than other accurate comparison methods. ProteinDBS v2.0 supports query by PDB protein ID and by new structures uploaded by users. To our knowledge, this is the only search engine that can simultaneously support global and local comparisons. ProteinDBS v2.0 is a useful tool to investigate functional or evolutional relationships among proteins. Moreover, the common substructures identified by local comparison can be potentially used to assist the human curation process in discovering new domains or folds from the ever-growing protein structure databases. The system is hosted at http://ProteinDBS.rnet.missouri.edu.

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

“…While there have been great advances in predicting protein structure from primary sequence (see later), the prediction of function from structure (let alone sequence) remains an important (if largely unattained) aim. [40][41][42][43][44][45][46][47][48][49][50][51][52][53][54] How much of sequence space is 'functional'?…”

CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval

“…Since direct comparison through experiments are not possible, we here make an effort to do an indirect comparison as follows. While presenting ProteinDBS in 15 the authors have claimed that it is 10.87 times faster than CE. Now, as has been reported in 21 , MASASW is more accurate and much more faster than CE.…”

“…The technique used in 14 has some similarities with our work which will be discussed in a later section. Subsequently, a second and enhanced version of the system called ProteinDBS v2.0 has been developed which is reported in 15 . ProteinDBS v2.0 incorporates the global comparison method using the knowledge-based feature extraction and online database indexing method of 16 and the local comparison method of 17 .…”