Identification of Secondary Binding Sites on Protein Surfaces for Rational Elaboration of Synthetic Protein Mimics

2021 ◽  
Author(s):  
Justin M. Torner ◽  
Yuwei Yang ◽  
David Rooklin ◽  
Yingkai Zhang ◽  
Paramjit S. Arora
Keyword(s):  
Binding Sites ◽  
Protein Surfaces ◽  
Protein Mimics ◽  
Synthetic Protein

scholarly journals PepSite: prediction of peptide-binding sites from protein surfaces

2012 ◽  
Vol 40 (W1) ◽  
pp. W423-W427 ◽  
Author(s):  
L. G. Trabuco ◽  
S. Lise ◽  
E. Petsalaki ◽  
R. B. Russell
Keyword(s):  
Binding Sites ◽  
Peptide Binding ◽  
Protein Surfaces

Empirical rules facilitate the search for binding sites on protein surfaces

2007 ◽  
Vol 25 (5) ◽  
pp. 671-679 ◽  
Author(s):  
Henrik te Heesen ◽  
Anna Melissa Schlitter ◽  
Jürgen Schlitter
Keyword(s):  
Binding Sites ◽  
Protein Surfaces

scholarly journals Predicting Peptide Binding Sites on Protein Surfaces by Clustering Chemical Interactions

2015 ◽  
Vol 108 (2) ◽  
pp. 215a
Author(s):  
Chengfei Yan ◽  
Xiaoqin Zou
Keyword(s):  
Binding Sites ◽  
Peptide Binding ◽  
Chemical Interactions ◽  
Protein Surfaces

Simple method for locating possible ligand binding sites on protein surfaces

1999 ◽  
Vol 20 (9) ◽  
pp. 983-988 ◽  
Author(s):  
Andrey A. Bliznyuk ◽  
Jill E. Gready
Keyword(s):  
Ligand Binding ◽  
Binding Sites ◽  
Simple Method ◽  
Protein Surfaces ◽  
Ligand Binding Sites

scholarly journals Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e40846 ◽  
Author(s):  
Keng-Chang Tsai ◽  
Jhih-Wei Jian ◽  
Ei-Wen Yang ◽  
Po-Chiang Hsu ◽  
Hung-Pin Peng ◽  
...  
Keyword(s):  
Probability Density ◽  
Binding Sites ◽  
Carbohydrate Binding ◽  
Protein Surfaces ◽  
3 Dimensional ◽  
Density Distributions ◽  
Probability Density Distributions ◽  
Interacting Atoms

scholarly journals Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1224
Author(s):  
Paula Jofily ◽  
Pedro G. Pascutti ◽  
Pedro H. M. Torres
Keyword(s):  
Binding Sites ◽  
Search Algorithm ◽  
Pose Prediction ◽  
Success Rates ◽  
Protein Surfaces ◽  
Cavity Detection ◽  
Docking Method ◽  
Potential Binding ◽  
Binding Pockets ◽  
Automated Pipeline

Probing protein surfaces to accurately predict the binding site and conformation of a small molecule is a challenge currently addressed through mainly two different approaches: blind docking and cavity detection-guided docking. Although cavity detection-guided blind docking has yielded high success rates, it is less practical when a large number of molecules must be screened against many detected binding sites. On the other hand, blind docking allows for simultaneous search of the whole protein surface, which however entails the loss of accuracy and speed. To bridge this gap, in this study, we developed and tested BLinDPyPr, an automated pipeline which uses FTMap and DOCK6 to perform a hybrid blind docking strategy. Through our algorithm, FTMap docked probe clusters are converted into DOCK6 spheres for determining binding regions. Because these spheres are solely derived from FTMap probes, their locations are contained in and specific to multiple potential binding pockets, which become the regions that are simultaneously probed and chosen by the search algorithm based on the properties of each candidate ligand. This method yields pose prediction results (45.2–54.3% success rates) comparable to those of site-specific docking with the classic DOCK6 workflow (49.7–54.3%) and is half as time-consuming as the conventional blind docking method with DOCK6.

Synthetic protein mimics: Structure of Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Acp-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe

Peptides ◽  
1992 ◽  
pp. 766-767
Author(s):  
Judith L. Flippen-Anderson ◽  
Isabella L. Karle
Keyword(s):  
Protein Mimics ◽  
Synthetic Protein

scholarly journals Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

PLoS ONE ◽  
2016 ◽  
Vol 11 (8) ◽  
pp. e0160315 ◽  
Author(s):  
Jhih-Wei Jian ◽  
Pavadai Elumalai ◽  
Thejkiran Pitti ◽  
Chih Yuan Wu ◽  
Keng-Chang Tsai ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Probability Density ◽  
Binding Sites ◽  
Protein Surfaces ◽  
3 Dimensional ◽  
Density Distributions ◽  
Ligand Binding Sites ◽  
Probability Density Distributions ◽  
Interacting Atoms

Modular design of synthetic protein mimics. Characterization of the helical conformation of a 13-residue peptide in crystals

Biochemistry ◽  
1989 ◽  
Vol 28 (16) ◽  
pp. 6696-6701 ◽  
Author(s):  
Isabella L. Karle ◽  
Judith L. Flippen-Anderson ◽  
K. Uma ◽  
P. Balaram
Keyword(s):  
Modular Design ◽  
Helical Conformation ◽  
Protein Mimics ◽  
Synthetic Protein

Organic solvents identify specific ligand binding sites on protein surfaces

1997 ◽  
Vol 15 (3) ◽  
pp. 264-268 ◽  
Author(s):  
Edvards Liepinsh ◽  
Gottfried Otting
Keyword(s):  
Ligand Binding ◽  
Organic Solvents ◽  
Binding Sites ◽  
Protein Surfaces ◽  
Ligand Binding Sites ◽  
Specific Ligand
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