Extraction of Protein Binding Pockets in Close Neighborhood of Bound Ligands Makes Comparisons Simple Due to Inherent Shape Similarity

2014 ◽  
Vol 54 (11) ◽  
pp. 3229-3237 ◽  
Author(s):  
Timo Krotzky ◽  
Thomas Rickmeyer ◽  
Thomas Fober ◽  
Gerhard Klebe
Keyword(s):  
Protein Binding ◽  
Shape Similarity ◽  
Binding Pockets

scholarly journals RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases

2009 ◽  
Vol 37 (Database) ◽  
pp. D369-D373 ◽  
Author(s):  
A. Shulman-Peleg ◽  
R. Nussinov ◽  
H. J. Wolfson
Keyword(s):  
Protein Binding ◽  
Binding Pockets ◽  
Nucleotide Bases

Incorporation of side chain flexibility into protein binding pockets using MTflex

2016 ◽  
Vol 24 (20) ◽  
pp. 4978-4987 ◽  
Author(s):  
Nupur Bansal ◽  
Zheng Zheng ◽  
Kenneth M. Merz
Keyword(s):  
Protein Binding ◽  
Side Chain ◽  
Chain Flexibility ◽  
Binding Pockets

scholarly journals Computational Analysis of HIV-1 Protease Protein Binding Pockets

2010 ◽  
Vol 50 (10) ◽  
pp. 1759-1771 ◽  
Author(s):  
Gene M. Ko ◽  
A. Srinivas Reddy ◽  
Sunil Kumar ◽  
Barbara A. Bailey ◽  
Rajni Garg
Keyword(s):  
Protein Binding ◽  
Computational Analysis ◽  
Binding Pockets ◽  
Hiv 1

scholarly journals Free enthalpies of replacing water molecules in protein binding pockets

2012 ◽  
Vol 26 (12) ◽  
pp. 1293-1309 ◽  
Author(s):  
Sereina Riniker ◽  
Luzi J. Barandun ◽  
François Diederich ◽  
Oliver Krämer ◽  
Andreas Steffen ◽  
...  
Keyword(s):  
Protein Binding ◽  
Water Molecules ◽  
Binding Pockets

scholarly journals TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets

2017 ◽  
Vol 45 (W1) ◽  
pp. W325-W330 ◽  
Author(s):  
Antonia Stank ◽  
Daria B. Kokh ◽  
Max Horn ◽  
Elena Sizikova ◽  
Rebecca Neil ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Protein Binding Site ◽  
Binding Pockets

Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real

2014 ◽  
Vol 55 (1) ◽  
pp. 165-179 ◽  
Author(s):  
Timo Krotzky ◽  
Christian Grunwald ◽  
Ute Egerland ◽  
Gerhard Klebe
Keyword(s):  
Protein Binding ◽  
Large Scale ◽  
Similar Protein ◽  
Binding Pockets

AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets

2020 ◽  
Vol 60 (9) ◽  
pp. 4326-4338 ◽  
Author(s):  
Siduo Jiang ◽  
Miklos Feher ◽  
Chris Williams ◽  
Brian Cole ◽  
David E. Shaw
Keyword(s):  
Protein Binding ◽  
Automated Method ◽  
Binding Pockets ◽  
Pharmacophore Models

scholarly journals Variation of geometrical and physicochemical properties in protein binding pockets and their ligands

2007 ◽  
Vol 8 (S8) ◽  
Author(s):  
Abdullah Kahraman ◽  
Richard J Morris ◽  
Roman A Laskowski ◽  
Janet M Thornton
Keyword(s):  
Protein Binding ◽  
Physicochemical Properties ◽  
Binding Pockets

Shape Variation in Protein Binding Pockets and their Ligands

2007 ◽  
Vol 368 (1) ◽  
pp. 283-301 ◽  
Author(s):  
Abdullah Kahraman ◽  
Richard J. Morris ◽  
Roman A. Laskowski ◽  
Janet M. Thornton
Keyword(s):  
Protein Binding ◽  
Shape Variation ◽  
Binding Pockets
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