Literature DB >> 11294795

ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions.

K S Thorn1, A A Bogan.   

Abstract

The Alanine Scanning Energetics database (ASEdb) is a searchable database of single alanine mutations in protein-protein, protein-nucleic acid, and protein-small molecule interactions for which binding affinities have been experimentally determined. In cases where structures are available, it contains surface areas of the mutated side chain and links to the PDB entries. It is useful for studying the contribution of single amino acids to the energetics of protein interactions, and can be updated by researchers as new data are generated.

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Year:  2001        PMID: 11294795     DOI: 10.1093/bioinformatics/17.3.284

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  116 in total

1.  A simple physical model for binding energy hot spots in protein-protein complexes.

Authors:  Tanja Kortemme; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2002-10-15       Impact factor: 11.205

2.  Structure-based method for analyzing protein-protein interfaces.

Authors:  Ying Gao; Renxiao Wang; Luhua Lai
Journal:  J Mol Model       Date:  2003-11-22       Impact factor: 1.810

3.  A hot-spot motif characterizes the interface between a designed ankyrin-repeat protein and its target ligand.

Authors:  Luthur Siu-Lun Cheung; Manu Kanwar; Marc Ostermeier; Konstantinos Konstantopoulos
Journal:  Biophys J       Date:  2012-02-07       Impact factor: 4.033

4.  Computational alanine scanning with linear scaling semiempirical quantum mechanical methods.

Authors:  David J Diller; Christine Humblet; Xiaohua Zhang; Lance M Westerhoff
Journal:  Proteins       Date:  2010-08-01

5.  A structure-based benchmark for protein-protein binding affinity.

Authors:  Panagiotis L Kastritis; Iain H Moal; Howook Hwang; Zhiping Weng; Paul A Bates; Alexandre M J J Bonvin; Joël Janin
Journal:  Protein Sci       Date:  2011-02-16       Impact factor: 6.725

6.  Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces.

Authors:  Brandon S Zerbe; David R Hall; Sandor Vajda; Adrian Whitty; Dima Kozakov
Journal:  J Chem Inf Model       Date:  2012-07-24       Impact factor: 4.956

7.  AB-Bind: Antibody binding mutational database for computational affinity predictions.

Authors:  Sarah Sirin; James R Apgar; Eric M Bennett; Amy E Keating
Journal:  Protein Sci       Date:  2015-11-06       Impact factor: 6.725

8.  Are protein-protein interfaces special regions on a protein's surface?

Authors:  Sam Tonddast-Navaei; Jeffrey Skolnick
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

9.  Conservation and relative importance of residues across protein-protein interfaces.

Authors:  Mainak Guharoy; Pinak Chakrabarti
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-12       Impact factor: 11.205

10.  How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues.

Authors:  Turkan Haliloglu; Ozlem Keskin; Buyong Ma; Ruth Nussinov
Journal:  Biophys J       Date:  2004-12-13       Impact factor: 4.033

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