Literature DB >> 19422931

Homology modeling in drug discovery: current trends and applications.

Claudio N Cavasotto1, Sharangdhar S Phatak.   

Abstract

As structural genomics (SG) projects continue to deposit representative 3D structures of proteins, homology modeling methods will play an increasing role in structure-based drug discovery. Although computational structure prediction methods provide a cost-effective alternative in the absence of experimental structures, developing accurate enough models still remains a big challenge. In this contribution, we report the current developments in this field, discuss in silico modeling limitations, and review the successful application of this technique to different stages of the drug discovery process.

Mesh:

Year:  2009        PMID: 19422931     DOI: 10.1016/j.drudis.2009.04.006

Source DB:  PubMed          Journal:  Drug Discov Today        ISSN: 1359-6446            Impact factor:   7.851


  108 in total

1.  Identification of lead compounds targeting the cathepsin B-like enzyme of Eimeria tenella.

Authors:  Marie Schaeffer; Joerg Schroeder; Anja R Heckeroth; Sandra Noack; Michael Gassel; Jeremy C Mottram; Paul M Selzer; Graham H Coombs
Journal:  Antimicrob Agents Chemother       Date:  2011-12-05       Impact factor: 5.191

2.  Genomewide Analysis of the Antimicrobial Peptides in Python bivittatus and Characterization of Cathelicidins with Potent Antimicrobial Activity and Low Cytotoxicity.

Authors:  Dayeong Kim; Nagasundarapandian Soundrarajan; Juyeon Lee; Hye-Sun Cho; Minkyeung Choi; Se-Yeoun Cha; Byeongyong Ahn; Hyoim Jeon; Minh Thong Le; Hyuk Song; Jin-Hoi Kim; Chankyu Park
Journal:  Antimicrob Agents Chemother       Date:  2017-08-24       Impact factor: 5.191

3.  Targeting the ubiquitin-conjugating enzyme E2D4 for cancer drug discovery-a structure-based approach.

Authors:  Vishwanath Ramatenki; Ramakrishna Dumpati; Rajender Vadija; Santhiprada Vellanki; Sarita Rajender Potlapally; Rohini Rondla; Uma Vuruputuri
Journal:  J Chem Biol       Date:  2016-12-24

Review 4.  From laptop to benchtop to bedside: structure-based drug design on protein targets.

Authors:  Lu Chen; John K Morrow; Hoang T Tran; Sharangdhar S Phatak; Lei Du-Cuny; Shuxing Zhang
Journal:  Curr Pharm Des       Date:  2012       Impact factor: 3.116

5.  Improving prediction of helix-helix packing in membrane proteins using predicted contact numbers as restraints.

Authors:  Bian Li; Jeffrey Mendenhall; Elizabeth Dong Nguyen; Brian E Weiner; Axel W Fischer; Jens Meiler
Journal:  Proteins       Date:  2017-04-01

6.  Identification of benzamide inhibitors of histone deacetylase 1 from Babesia and Theileria species via high-throughput virtual screening and molecular dynamics simulations.

Authors:  Merve Gurboga; Gizem Kugu; Hiqmet Kamberaj; Ozal Mutlu
Journal:  Parasitol Res       Date:  2021-05-14       Impact factor: 2.289

7.  Mastering tricyclic ring systems for desirable functional cannabinoid activity.

Authors:  Ravil R Petrov; Lindsay Knight; Shao-Rui Chen; Jim Wager-Miller; Steven W McDaniel; Fanny Diaz; Francis Barth; Hui-Lin Pan; Ken Mackie; Claudio N Cavasotto; Philippe Diaz
Journal:  Eur J Med Chem       Date:  2013-09-29       Impact factor: 6.514

8.  Benchmarking GPCR homology model template selection in combination with de novo loop generation.

Authors:  Gregory L Szwabowski; Paige N Castleman; Chandler K Sears; Lee H Wink; Judith A Cole; Daniel L Baker; Abby L Parrill
Journal:  J Comput Aided Mol Des       Date:  2020-07-31       Impact factor: 3.686

Review 9.  Modelling three-dimensional protein structures for applications in drug design.

Authors:  Tobias Schmidt; Andreas Bergner; Torsten Schwede
Journal:  Drug Discov Today       Date:  2013-11-08       Impact factor: 7.851

10.  Exploring 3D structure of human gonadotropin hormone receptor at antagonist state using homology modeling, molecular dynamic simulation, and cross-docking studies.

Authors:  Amirhossein Sakhteman; Minasadat Khoddami; Manica Negahdaripour; Arash Mehdizadeh; Mohsen Tatar; Younes Ghasemi
Journal:  J Mol Model       Date:  2016-08-25       Impact factor: 1.810

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