Interactive JIMD articles using the iSee concept: turning a new page on structural biology data

Lee, Wen‐Hwa; Yue, Wyatt W.; Raush, Eugene; Totrov, Maxim; Abagyan, Ruben; Oppermann, U.

doi:10.1007/s10545-011-9334-4

Cited by 6 publications

(4 citation statements)

References 10 publications

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“…In line with the urgency, results were made available online immediately for download. In addition, since exploring 3D data requires specialised tools 52,53 , hits were made accessible on the Fragalysis webtool (https://fragalysis.diamond.ac.uk) that allows easy exploration of the hits in interactive 3D.…”

Section: Discussionmentioning

confidence: 99%

Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease

et al. 2020

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COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.

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Section: Discussionmentioning

confidence: 99%

Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease

et al. 2020

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“…ActiveICM is widely accepted and used by the computational and structural biology communities as an advanced format for 3D data visualization. [73, 74] In the PeptiSite pages, the molecular entities forming the binding site are consistently color-coded according to their type (e.g. polypeptide receptor chains, co-factors, metal ions, or the ligands) and are presented in several convenient and informative views, which are controlled by the links on the left side of the screen, in the pocket and site tabs.…”

Section: Peptisite Accessmentioning

confidence: 99%

PeptiSite: A structural database of peptide binding sites in 4D

Acharya

Kufareva

Ilatovskiy

et al. 2014

Biochemical and Biophysical Research Communications

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We developed PeptiSite, a comprehensive and reliable database of biologically and structurally characterized peptide-binding sites, in which each site is represented by an ensemble of its complexes with protein, peptide and small molecule partners. The unique features of the database include (1) the ensemble site representation that provides a fourth dimension to the otherwise three dimensional data, (2) comprehensive characterization of the binding site architecture that may consist of a multimeric protein assembly with cofactors and metal ions (3) analysis of consensus interaction motifs within the ensembles and identification of conserved determinants of these interactions. Currently the database contains 585 proteins with 650 peptide-binding sites. http://ablab.ucsd.edu/~chayan/PeptiSite link allows searching for the sites of interest and interactive visualization of the ensembles using the ActiveICM web-browser plugin. This structural database for protein-peptide interactions enables understanding of structural principles of these interactions and may assist the development of an efficient peptide docking benchmark.

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“…ActiveICM version 1.1-6 or higher is required to access all the functionality of the Pocketome pages. ActiveICM is widely accepted and used by the computational and structural biology communities as an advanced format for 3D data visualization (27,28). In the Pocketome pages, the molecular entities forming the binding site are consistently color coded according to their type (e.g.…”

Section: Pocketome Accessmentioning

confidence: 99%

Pocketome: an encyclopedia of small-molecule binding sites in 4D

Kufareva

Ilatovskiy

Abagyan

2011

Nucleic Acids Research

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159

144

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The importance of binding site plasticity in protein–ligand interactions is well-recognized, and so are the difficulties in predicting the nature and the degree of this plasticity by computational means. To assist in understanding the flexible protein–ligand interactions, we constructed the Pocketome, an encyclopedia of about one thousand experimentally solved conformational ensembles of druggable binding sites in proteins, grouped by location and consistent chain/cofactor composition. The multiplicity of pockets within the ensembles adds an extra, fourth dimension to the Pocketome entry data. Within each ensemble, the pockets were carefully classified by the degree of their pairwise similarity and compatibility with different ligands. The core of the Pocketome is derived regularly and automatically from the current releases of the Protein Data Bank and the Uniprot Knowledgebase; this core is complemented by entries built from manually provided seed ligand locations. The Pocketome website (www.pocketome.org) allows searching for the sites of interest, analysis of conformational clusters, important residues, binding compatibility matrices and interactive visualization of the ensembles using the ActiveICM web browser plugin. The Pocketome collection can be used to build multi-conformational docking and 3D activity models as well as to design cross-docking and virtual ligand screening benchmarks.

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Interactive JIMD articles using the iSee concept: turning a new page on structural biology data

Cited by 6 publications

References 10 publications

Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease

Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease

PeptiSite: A structural database of peptide binding sites in 4D

Pocketome: an encyclopedia of small-molecule binding sites in 4D

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