A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys

Y. Chen

doi:10.1093/nar/gkh785

A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys

Nucleic Acids Research ◽

10.1093/nar/gkh785 ◽

2004 ◽

Vol 32 (17) ◽

pp. 5147-5162 ◽

Cited By ~ 58

Author(s):

Y. Chen

Keyword(s):

Hydrogen Bonding ◽

Hydrogen Bonding Potential

Download Full-text

Double zipper helical assembly of deoxyoligonucleotides: mutual templating and chiral imprinting to form hybrid DNA ensembles

Chemical Communications ◽

10.1039/c4cc06759b ◽

2015 ◽

Vol 51 (25) ◽

pp. 5493-5496 ◽

Cited By ~ 12

Author(s):

Nagarjun Narayanaswamy ◽

Gorle Suresh ◽

U. Deva Priyakumar ◽

T. Govindaraju

Keyword(s):

Hydrogen Bonding ◽

Ambient Conditions ◽

Hydrogen Bonding Potential ◽

Hybrid Dna

Herein, the conventional and unconventional hydrogen bonding potential of adenine in APA for double zipper helical assembly of deoxyoligonucleotides is demonstrated under ambient conditions.

Download Full-text

Changing the hydrogen-bonding potential in the DNA binding site of EcoRI by site-directed mutagenesis drastically reduces the enzymic activity, not, however, the preference of this restriction endonuclease for cleavage within the site -GAATTC-

Biochemistry ◽

10.1021/bi00432a047 ◽

1989 ◽

Vol 28 (6) ◽

pp. 2678-2684 ◽

Cited By ~ 57

Author(s):

Jurgen Alves ◽

Thomas Rueter ◽

Robert Geiger ◽

Anja Fliess ◽

Guenter Maass ◽

...

Keyword(s):

Hydrogen Bonding ◽

Dna Binding ◽

Binding Site ◽

Restriction Endonuclease ◽

Enzymic Activity ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Dna Binding Site ◽

Hydrogen Bonding Potential

Download Full-text

Satisfying Hydrogen Bonding Potential in Proteins

Journal of Molecular Biology ◽

10.1006/jmbi.1994.1334 ◽

1994 ◽

Vol 238 (5) ◽

pp. 777-793 ◽

Cited By ~ 1472

Author(s):

Ian K. McDonald ◽

Janet M. Thornton

Keyword(s):

Hydrogen Bonding ◽

Hydrogen Bonding Potential

Download Full-text

The synthesis of antiviral compounds with ambivalent hydrogen bonding potential

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc1993s029 ◽

1993 ◽

Vol 58 (s1) ◽

pp. 29-32

Author(s):

D. Loakes ◽

Daniel M. Brown

Keyword(s):

Hydrogen Bonding ◽

Antiviral Compounds ◽

Hydrogen Bonding Potential

Download Full-text

Faculty Opinions recommendation of An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1012507.185970 ◽

2003 ◽

Author(s):

Janet Thornton

Keyword(s):

Hydrogen Bonding ◽

Protein Complexes ◽

Hydrogen Bonding Potential

Download Full-text

An Empirical Backbone−Backbone Hydrogen-Bonding Potential in Proteins and Its Applications to NMR Structure Refinement and Validation

Journal of the American Chemical Society ◽

10.1021/ja0319994 ◽

2004 ◽

Vol 126 (23) ◽

pp. 7281-7292 ◽

Cited By ~ 85

Author(s):

Alexander Grishaev ◽

Ad Bax

Keyword(s):

Hydrogen Bonding ◽

Structure Refinement ◽

Nmr Structure ◽

Hydrogen Bonding Potential

Download Full-text

Physicochemical Determinants of Passive Membrane Permeability: Role of Solute Hydrogen-Bonding Potential and Volume.

Journal of Medicinal Chemistry ◽

10.1021/jm0200963 ◽

2002 ◽

Vol 45 (10) ◽

pp. 2122-2122 ◽

Cited By ~ 1

Author(s):

Jay T. Goodwin ◽

Robert A. Conradi ◽

Norman F. H. Ho ◽

Philip S. Burton

Keyword(s):

Hydrogen Bonding ◽

Membrane Permeability ◽

Hydrogen Bonding Potential ◽

Passive Membrane

Download Full-text

Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein–Ligand Interactions

Journal of Chemical Information and Modeling ◽

10.1021/ci2003939 ◽

2011 ◽

Vol 51 (11) ◽

pp. 2994-3004 ◽

Cited By ~ 12

Author(s):

Mingyue Zheng ◽

Bing Xiong ◽

Cheng Luo ◽

Shanshan Li ◽

Xian Liu ◽

...

Keyword(s):

Hydrogen Bonding ◽

Drug Design ◽

Scoring Functions ◽

Two Dimensional ◽

Knowledge Based ◽

Protein Ligand Interactions ◽

Ligand Interactions ◽

Hydrogen Bonding Potential

Download Full-text

Functionalized proline with double hydrogen bonding potential: highly enantioselective Michael addition of carbonyl compounds to β-nitrostyrenes in brine

Tetrahedron Letters ◽

10.1016/j.tetlet.2010.07.164 ◽

2010 ◽

Vol 51 (40) ◽

pp. 5281-5286 ◽

Cited By ~ 27

Author(s):

Satyajit Saha ◽

Saona Seth ◽

Jarugu Narasimha Moorthy

Keyword(s):

Hydrogen Bonding ◽

Michael Addition ◽

Carbonyl Compounds ◽

Hydrogen Bonding Potential ◽

Double Hydrogen

Download Full-text

The HYBOT 3D MF Application and it Integration with CoMFA

Biomedical Chemistry Research and Methods ◽

10.18097/bmcrm00073 ◽

2018 ◽

Vol 1 (3) ◽

pp. e00073

Author(s):

V.S. Skvortsov ◽

A.V. Mikurova ◽

O.A. Raevsky

Keyword(s):

Hydrogen Bonding ◽

Predictive Power ◽

Chemical Compounds ◽

It Integration ◽

Hydrogen Bonding Potential

The program “HYBOT 3D MF” based on the potential “6-8” modified by using HYBOT hydrogen bonding factors has been developed. An integration with “QSAR and Advanced CoMFA” module of the SYBYL-X is performed by set of macros written in SPL. A full working version of the program is available at http://www.ibmc.msk.ru/HYBOT3D. For a number of sets of chemical compounds having pronounced differences in groups with the hydrogen bonding potential, the use of HYBOT 3D MF fields makes it possible to improve the predictive power of models created by the CoMFA technology.

Download Full-text