<i>Fragment Finder 2.0</i>: a computing server to identify structurally similar fragments

Nagarajan, Ramya; Balan, S.; Sabarinathan, Radhakrishnan; Vaishnavi, Marthandan Kirti; Sekar, K.

doi:10.1107/s0021889812001501

Cited by 5 publications

(3 citation statements)

References 23 publications

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“…Such a numbering scheme may be used in order to preserve the homology. The reference protein may be numbered sequentially starting with 1, then the homologous protein from another species aligned to it (Balamurugan et al, 2007;Kumar & Sekar, 2010;Nagarajan et al, 2012). If residues are not present in the homologous sequence, residue numbers may be skipped so that alignment can be preserved (Kumar et al, 2009;Balamurugan et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

IMRPS: Inserted and Modified Residues in Protein Structures. A database

et al. 2020

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Modified residues present in proteins are the result of post‐translational modifications (PTMs). These PTMs increase the functional diversity of the proteome and influence various biological processes and diseased conditions. Therefore, identification and understanding of PTMs in various protein structures is of great significance. In view of this, an online database, Inserted and Modified Residues in Protein Structures (IMRPS), has been developed. IMRPS is a derived database that furnishes information on the residues modified and inserted in the protein structures available in the Protein Data Bank (PDB). The database is equipped with a graphical user interface and has an option to view the data for non‐redundant protein structures (25 and 90%) as well. A quality criteria cutoff has been incorporated to assist in displaying the specific set of PDB codes. The entire protein structure along with the inserted or modified residues can be visualized in JSmol. This database will be updated regularly (presently, every three months) and can be accessed through the URL http://cluster.physics.iisc.ac.in/imrps/.

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Section: Introductionmentioning

confidence: 99%

IMRPS: Inserted and Modified Residues in Protein Structures. A database

et al. 2020

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“…In X-ray crystallographic experiments, and thus in many of the three-dimensional structures deposited in the PDB, the loops and ends of the polypeptide chains and certain residues in the middle portion of the chain are not observed owing to poor electron density (Sumathi et al, 2006;Saravanan et al, 2010;Djinovic Carugo & Carugo, 2015;Gurusaran et al, 2016). Thus, these regions will not be available in the atomic coordinates file submitted to the PDB and they are referred to as 'missing regions' (Ananthalakshmi, Kumar et al, 2005;Ananthalakshmi, Samayamohan et al, 2005;Nagarajan et al, 2012;Santhosh et al, 2019). Depending on the location of the missing regions in a polypeptide chain, they can be classified into three categories: 'N-terminal' at the beginning of the polypeptide chain, 'C-terminal' at the end of the polypeptide chain, and 'Middle' anywhere between N-terminal and C-terminal.…”

Section: Introductionmentioning

confidence: 99%

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

et al. 2019

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Missing regions in protein crystal structures are those regions that cannot be resolved, mainly owing to poor electron density (if the three‐dimensional structure was solved using X‐ray crystallography). These missing regions are known to have high B factors and could represent loops with a possibility of being part of an active site of the protein molecule. Thus, they are likely to provide valuable information and play a crucial role in the design of inhibitors and drugs and in protein structure analysis. In view of this, an online database, Missing Regions in Polypeptide Chains (MRPC), has been developed which provides information about the missing regions in protein structures available in the Protein Data Bank. In addition, the new database has an option for users to obtain the above data for non‐homologous protein structures (25 and 90%). A user‐friendly graphical interface with various options has been incorporated, with a provision to view the three‐dimensional structure of the protein along with the missing regions using JSmol. The MRPC database is updated regularly (currently once every three months) and can be accessed freely at the URL http://cluster.physics.iisc.ac.in/mrpc.

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“…Superimposé ( 5 ) combines several search algorithms such as TM-align ( 11 ) or CE ( 12 ) to search for fragments similar to a query. The FragFinder ( 6 ) search engine is based on the comparison of the main chain backbone conformational angles (ϕ and ψ). SA-Mot ( 7 ) is based on the encoding of structure as strings of a structural alphabet to search for over-represented conformations among collections of proteins with similar functions.…”

Section: Introductionmentioning

confidence: 99%

BCSearch: fast structural fragment mining over large collections of protein structures

et al. 2015

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Resources to mine the large amount of protein structures available today are necessary to better understand how amino acid variations are compatible with conformation preservation, to assist protein design, engineering and, further, the development of biologic therapeutic compounds. BCSearch is a versatile service to efficiently mine large collections of protein structures. It relies on a new approach based on a Binet–Cauchy kernel that is more discriminative than the widely used root mean square deviation criterion. It has statistics independent of size even for short fragments, and is fast. The systematic mining of large collections of structures such as the complete SCOPe protein structural classification or comprehensive subsets of the Protein Data Bank can be performed in few minutes. Based on this new score, we propose four innovative applications: BCFragSearch and BCMirrorSearch, respectively, search for fragments similar and anti-similar to a query and return information on the diversity of the sequences of the hits. BCLoopSearch identifies candidate fragments of fixed size matching the flanks of a gaped structure. BCSpecificitySearch analyzes a complete protein structure and returns information about sites having few similar fragments. BCSearch is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/BCSearch.

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Fragment Finder 2.0: a computing server to identify structurally similar fragments

Cited by 5 publications

References 23 publications

IMRPS: Inserted and Modified Residues in Protein Structures. A database

IMRPS: Inserted and Modified Residues in Protein Structures. A database

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

BCSearch: fast structural fragment mining over large collections of protein structures

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