2009
DOI: 10.1021/ci8003094
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Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity

Abstract: The large volume of protein-ligand structures now available enables innovative and efficient protocols in computational FBDD (Fragment-Based Drug Design) to be proposed based on experimental data. In this work, we build a database of MED-Portions, where a MED-Portion is a new structural object encoding protein-fragment binding sites. MED-Portions are derived from mining all available protein-ligand structures with any library of small molecules. Combined with the MED-SuMo software to superpose similar protein … Show more

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Cited by 42 publications
(38 citation statements)
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“…As the knowledge of the three dimensional structures of proteins has the potential to accelerate drug discovery (Congreve et al, 2005;DoppeltAzeroual et al, 2009), recent developments in bioinformatics that mainly aim in filling the gap between sequence and structure space, have greatly transformed this research area (Doppelt et al, 2007;Hajduk, 2006;Moriaud et al, 2009). Thus, our work could be supportive in such approaches.…”
Section: Resultsmentioning
confidence: 73%
“…As the knowledge of the three dimensional structures of proteins has the potential to accelerate drug discovery (Congreve et al, 2005;DoppeltAzeroual et al, 2009), recent developments in bioinformatics that mainly aim in filling the gap between sequence and structure space, have greatly transformed this research area (Doppelt et al, 2007;Hajduk, 2006;Moriaud et al, 2009). Thus, our work could be supportive in such approaches.…”
Section: Resultsmentioning
confidence: 73%
“…16,60,61,64 Its main advantage is to detect binding sites with similar or related binding modes which could not be identified using rigid (or even flexible) superimposition approaches. Its heuristic is based on a 3D representation of macromolecule structures using precise Structural Chemical Features (SCFs).…”
Section: Med-sumo Algorithmmentioning
confidence: 99%
“…The full surface database which contains whole surfaces of the protein structures and the MED-Portions database also containing small protein regions but where characterized by chemical fragments detected in the ligands or peptides from the PDB. 16,17 The original version of SuMo is available on the internet, 61 but the latest improvements are only included in the MED-SuMo software distributed by MEDIT SA. 62 These improvements concern the definition and conception of protein databases and as well as the heuristic itself.…”
Section: Med-sumo Algorithmmentioning
confidence: 99%
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“…Caveat [12] and HOOK [13] were among the first ''fragment-linking'' computational approaches developed in the early 1990s. Newer generation computational methods continue to be developed (e.g., Re-core [14], Allegrow (Boston De Novo Design, Boston, MA, 2009), Confirm [15], MED-SuMo [16], and pharmacophore modeling for scaffold replacement in MOE (Chemical Computing Group, Montreal, Canada, 2009)) and successful uses of these newer programs are being reported.…”
mentioning
confidence: 99%