abagyan.ucsd.edu abagyan.ucsd.edu

abagyan.ucsd.edu

Abagyan Lab

Molecular Modeling and Bioinformatics. Ligand docking and drug discovery. Protein-protein docking and interface prediction. Binding pockets as drug targets. Website Of The Abagyan Lab. We dock compounds, proteins and peptides, do protein modeling, structure based lead discovery, drug repurposing, cheminformatics, molecular design, structural modeling and drug binding for GPCRs, kinases, nuclear receptors, green chemistry, structural basis of adverse effects. And the San Diego Supercomputer Center. Struct...

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Molecular Modeling and Bioinformatics. Ligand docking and drug discovery. Protein-protein docking and interface prediction. Binding pockets as drug targets. Website Of The Abagyan Lab. We dock compounds, proteins and peptides, do protein modeling, structure based lead discovery, drug repurposing, cheminformatics, molecular design, structural modeling and drug binding for GPCRs, kinases, nuclear receptors, green chemistry, structural basis of adverse effects. And the San Diego Supercomputer Center. Struct...
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Abagyan Lab | abagyan.ucsd.edu Reviews

https://abagyan.ucsd.edu

Molecular Modeling and Bioinformatics. Ligand docking and drug discovery. Protein-protein docking and interface prediction. Binding pockets as drug targets. Website Of The Abagyan Lab. We dock compounds, proteins and peptides, do protein modeling, structure based lead discovery, drug repurposing, cheminformatics, molecular design, structural modeling and drug binding for GPCRs, kinases, nuclear receptors, green chemistry, structural basis of adverse effects. And the San Diego Supercomputer Center. Struct...

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abagyan.ucsd.edu abagyan.ucsd.edu
1

PIER: Protein IntErface Recognition Server

http://abagyan.ucsd.edu/PIER

Chain(s) (e.g: a,b):. We demonstrated that adding the evolutionary conservation signal only marginally influenced the overall prediction performance on the benchmark; moreover, for certain classes of proteins, using this signal actually resulted in a deteriorated prediction. Thorough benchmarking using other datasets from literature showed that PIER yielded improved performance as compared to several alignment-free or alignment-dependent predictions.

2

GPCRDock2013: Home Page

http://abagyan.ucsd.edu/GPCRDock2013

A bitopic (orthosteric/allosteric) small molecule agonist in a pocket with closely homologous template structures available. View results ». A bitopic (orthosteric/allosteric) arrestin-biased agonist in a pocket with closely homologous template structures available. View results ». A small molecule antagonist in a pocket with only extremely distant templates available. View results ». A small molecule antagonist in a pocket with only extremely distant templates available. View results ».

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pocketome.org pocketome.org

Pocketome

http://www.pocketome.org/index.cgi?act=abstract

Ligand PDB Het IDs. 2011–2016 Abagyan Lab. The Pocketome [Ref. 1]. Is an encyclopedia of conformational ensembles of druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry describes a site on a protein surface that is involved in transient interactions with small molecules and peptides. The automatic Pocketome generation procedure includes only proteins that (i) have an entry in the reviewed part of the Uniprot. The Pocketom...

pocketome.org pocketome.org

Pocketome

http://www.pocketome.org/index.cgi?act=browseall

Ligand PDB Het IDs. 2011–2016 Abagyan Lab. X2060;Other mammals;. X2060;Gram-positive bacteria;. X2060;Gram-negative bacteria;. 1433C TOBAC 1 252. 14-3-3-like protein C [14-3-3 family]. 1o9c, 1o9d, 1o9e, 1o9f, 2o98, 3e6y, 3m50, 3m51. Cw1, ebt, fsc, yr1. 1433S HUMAN 1 233. 14-3-3 protein sigma [14-3-3 family]. 0dv, 0kb, 0kc, 0kg, 0kh, 0v4, 1ct, 2ct, ca, cw7, fc7, fja, fsc, fw1, m1t, plp, sep, tpo, y03, y04, y06, y07, y09. 1433Z HUMAN 1 244 pep. 14-3-3 protein zeta/delta [14-3-3 family]. 1A12 SOLLC 11 438.

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Molecular Modeling and Bioinformatics. Ligand docking and drug discovery. Protein-protein docking and interface prediction. Binding pockets as drug targets. Website Of The Abagyan Lab. We dock compounds, proteins and peptides, do protein modeling, structure based lead discovery, drug repurposing, cheminformatics, molecular design, structural modeling and drug binding for GPCRs, kinases, nuclear receptors, green chemistry, structural basis of adverse effects. And the San Diego Supercomputer Center. Struct...

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