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Protocols

ASEdb specifications

Information


Unique identifier OMICS_15557
Name ASEdb
Alternative name Alanine Scanning Energetics database
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Kurt Thorn

Publication for Alanine Scanning Energetics database

ASEdb citations

 (11)
library_books

Predicting hot spots in protein interfaces based on protrusion index, pseudo hydrophobicity and electron ion interaction pseudopotential features

2016
Oncotarget
PMCID: 4951271
PMID: 26934646
DOI: 10.18632/oncotarget.7695

[…] free energy resulting from the mutations of protein residues to alanine within a protein interface. A database collecting a list of hot spots identified by alanine scanning mutagenesis experiments is Alanine Scanning Energetics Database (ASEdb) []. Binding Interface Database (BID) is another database which contains experimentally verified hot spots from literature studies [].The characteristics of […]

call_split

Co Occurring Atomic Contacts for the Characterization of Protein Binding Hot Spots

2015
PLoS One
PMCID: 4684219
PMID: 26675422
DOI: 10.1371/journal.pone.0144486
call_split See protocol

[…] The training dataset in this work contains 20 protein complexes, most of which are collected from the ASEdb database [], denoted herein as the ASEdb dataset. Interfacial mutations for these complexes are defined by FoldX for the sake of making a fair performance comparison with FoldX and other existin […]

library_books

The Contribution of Missense Mutations in Core and Rim Residues of Protein–Protein Interfaces to Human Disease

2015
J Mol Biol
PMCID: 4548493
PMID: 26173036
DOI: 10.1016/j.jmb.2015.07.004

[…] e threshold of statistical significance, possibly because of the paucity of data and, thus, need to be confirmed on a larger set of protein interfaces.Early work on five protein complexes reported in ASEdb suggested that mutations in the interface rim are silent or moderately affect the binding energy of the complex (ΔΔG < 2 kcal/mol), whereas mutations with the most deleterious effect on binding […]

library_books

Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein Protein Interactions

2015
PMCID: 4518475
PMID: 26091166
DOI: 10.1016/j.chembiol.2015.04.019

[…] verarch the two (). There are a number of methods for identifying hotspot regions at protein surfaces (), commonly assessed by their ability to recapitulate experimental data from sources such as the ASEdb alanine scanning energetics database (), the BID (Binding Interface Database) (), and the HotSprint database (). The first class of methods is empirical and correlates experimental data with sur […]

library_books

Integrating water exclusion theory into βcontacts to predict binding free energy changes and binding hot spots

2014
BMC Bioinformatics
PMCID: 3941611
PMID: 24568581
DOI: 10.1186/1471-2105-15-57

[…] te the difference of the binding hot spot prediction results by βACV ASA , FoldX and Robetta. The 3HFM complex is an antibody-antigen binding between HyHEL-10 and hen egg white lysozyme. According to ASEdb, a total of 25 alanine mutations were experimented, 11 of which have ΔΔG more than 2 kcal/mol.Our βACV ASA correctly identified 9 binding hot spot residues with a recall of 0.818, but made 3 fa […]

library_books

Genome wide structural modelling of TCR pMHC interactions

2013
BMC Genomics
PMCID: 3852114
PMID: 24564684
DOI: 10.1186/1471-2164-14-S5-S5

[…] To determine the contribution of a residue to the binding affinity, the alanine-scanning mutagenesis is frequently used as an experimental probe. We selected 70 mutated residues collected from the ASEdb [] with 4 Ag-Ab complexes whose 3D structures were known. Those mutated residues should position at protein-protein interfaces and be the contact residues. Based on the interacting characteristi […]

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ASEdb institution(s)
Graduate Group in Biophysics, University of California, San Francisco, CA, USA
ASEdb funding source(s)
Supported by a Howard Hughes Medical Institute Predoctoral Fellowship, by a National Defense Science and Engineering Graduate Fellowship from the United States Department of Defense and by the Lloyd M. Kozloff Fellowship.

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