Literature DB >> 22922346

Computational drug discovery.

Si-Sheng Ou-Yang1, Jun-Yan Lu, Xiang-Qian Kong, Zhong-Jie Liang, Cheng Luo, Hualiang Jiang.   

Abstract

Computational drug discovery is an effective strategy for accelerating and economizing drug discovery and development process. Because of the dramatic increase in the availability of biological macromolecule and small molecule information, the applicability of computational drug discovery has been extended and broadly applied to nearly every stage in the drug discovery and development workflow, including target identification and validation, lead discovery and optimization and preclinical tests. Over the past decades, computational drug discovery methods such as molecular docking, pharmacophore modeling and mapping, de novo design, molecular similarity calculation and sequence-based virtual screening have been greatly improved. In this review, we present an overview of these important computational methods, platforms and successful applications in this field.

Mesh:

Year:  2012        PMID: 22922346      PMCID: PMC4003107          DOI: 10.1038/aps.2012.109

Source DB:  PubMed          Journal:  Acta Pharmacol Sin        ISSN: 1671-4083            Impact factor:   6.150


  85 in total

1.  GAsDock: a new approach for rapid flexible docking based on an improved multi-population genetic algorithm.

Authors:  Honglin Li; Chunlian Li; Chunshan Gui; Xiaomin Luo; Kaixian Chen; Jianhua Shen; Xicheng Wang; Hualiang Jiang
Journal:  Bioorg Med Chem Lett       Date:  2004-09-20       Impact factor: 2.823

2.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

Authors:  Richard A Friesner; Jay L Banks; Robert B Murphy; Thomas A Halgren; Jasna J Klicic; Daniel T Mainz; Matthew P Repasky; Eric H Knoll; Mee Shelley; Jason K Perry; David E Shaw; Perry Francis; Peter S Shenkin
Journal:  J Med Chem       Date:  2004-03-25       Impact factor: 7.446

3.  Knowledge-based scoring functions in drug design. 1. Developing a target-specific method for kinase-ligand interactions.

Authors:  Mengzhu Xue; Mingyue Zheng; Bing Xiong; Yanlian Li; Hualiang Jiang; Jingkang Shen
Journal:  J Chem Inf Model       Date:  2010-08-23       Impact factor: 4.956

Review 4.  Predicting protein druggability.

Authors:  Philip J Hajduk; Jeffrey R Huth; Christin Tse
Journal:  Drug Discov Today       Date:  2005-12       Impact factor: 7.851

5.  Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation.

Authors:  Jianhua Cai; Cong Han; Tiancen Hu; Jian Zhang; Dalei Wu; Fangdao Wang; Yunqing Liu; Jianping Ding; Kaixian Chen; Jianmin Yue; Xu Shen; Hualiang Jiang
Journal:  Protein Sci       Date:  2006-08-01       Impact factor: 6.725

Review 6.  Lysophospholipid receptors as potential drug targets in tissue transplantation and autoimmune diseases.

Authors:  Jerold Chun; Hugh Rosen
Journal:  Curr Pharm Des       Date:  2006       Impact factor: 3.116

Review 7.  Molecular mechanisms of chemopreventive effects of selected dietary and medicinal phenolic substances.

Authors:  Y Surh
Journal:  Mutat Res       Date:  1999-07-16       Impact factor: 2.433

8.  Finding a way out: lymphocyte egress from lymphoid organs.

Authors:  Susan R Schwab; Jason G Cyster
Journal:  Nat Immunol       Date:  2007-12       Impact factor: 25.606

9.  Molecular drug targets and structure based drug design: A holistic approach.

Authors:  Shailza Singh; Balwant Kumar Malik; Durlabh Kumar Sharma
Journal:  Bioinformation       Date:  2006-12-23

10.  Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation.

Authors:  Xiaofeng Liu; Fang Bai; Sisheng Ouyang; Xicheng Wang; Honglin Li; Hualiang Jiang
Journal:  BMC Bioinformatics       Date:  2009-03-31       Impact factor: 3.169

View more
  53 in total

1.  Constructing and characterizing a bioactive small molecule and microRNA association network for Alzheimer's disease.

Authors:  Fanlin Meng; Enyu Dai; Xuexin Yu; Yan Zhang; Xiaowen Chen; Xinyi Liu; Shuyuan Wang; Lihua Wang; Wei Jiang
Journal:  J R Soc Interface       Date:  2013-12-18       Impact factor: 4.118

2.  Novel dihydropyrimidine derivatives as potential HDAC inhibitors: in silico study.

Authors:  Ganapathi Thipparapu; Rajanna Ajumeera; Vijayalakshmi Venkatesan
Journal:  In Silico Pharmacol       Date:  2017-10-12

Review 3.  An overview of recent molecular dynamics applications as medicinal chemistry tools for the undruggable site challenge.

Authors:  Ugo Perricone; Maria Rita Gulotta; Jessica Lombino; Barbara Parrino; Stella Cascioferro; Patrizia Diana; Girolamo Cirrincione; Alessandro Padova
Journal:  Medchemcomm       Date:  2018-04-19       Impact factor: 3.597

4.  Celebrating the 80th anniversary of the Shanghai Institute of Materia Medica, Chinese Academy of Sciences (SIMM).

Authors:  Jian Ding
Journal:  Acta Pharmacol Sin       Date:  2012-09       Impact factor: 6.150

5.  Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches.

Authors:  Eckart Bindewald; Kirill A Afonin; Mathias Viard; Paul Zakrevsky; Taejin Kim; Bruce A Shapiro
Journal:  Nano Lett       Date:  2016-02-29       Impact factor: 11.189

Review 6.  CANDO and the infinite drug discovery frontier.

Authors:  Mark Minie; Gaurav Chopra; Geetika Sethi; Jeremy Horst; George White; Ambrish Roy; Kaushik Hatti; Ram Samudrala
Journal:  Drug Discov Today       Date:  2014-06-26       Impact factor: 7.851

7.  Rapid activity prediction of HIV-1 integrase inhibitors: harnessing docking energetic components for empirical scoring by chemometric and artificial neural network approaches.

Authors:  Patcharapong Thangsunan; Sila Kittiwachana; Puttinan Meepowpan; Nawee Kungwan; Panchika Prangkio; Supa Hannongbua; Nuttee Suree
Journal:  J Comput Aided Mol Des       Date:  2016-06-17       Impact factor: 3.686

8.  Drug screening strategy for human membrane proteins: from NMR protein backbone structure to in silica- and NMR-screened hits.

Authors:  Steffen Lindert; Innokentiy Maslennikov; Ellis J C Chiu; Levi C Pierce; J Andrew McCammon; Senyon Choe
Journal:  Biochem Biophys Res Commun       Date:  2014-02-10       Impact factor: 3.575

9.  Benchmarking methods and data sets for ligand enrichment assessment in virtual screening.

Authors:  Jie Xia; Ermias Lemma Tilahun; Terry-Elinor Reid; Liangren Zhang; Xiang Simon Wang
Journal:  Methods       Date:  2014-12-03       Impact factor: 3.608

10.  Free energy landscape for the binding process of Huperzine A to acetylcholinesterase.

Authors:  Fang Bai; Yechun Xu; Jing Chen; Qiufeng Liu; Junfeng Gu; Xicheng Wang; Jianpeng Ma; Honglin Li; José N Onuchic; Hualiang Jiang
Journal:  Proc Natl Acad Sci U S A       Date:  2013-02-25       Impact factor: 11.205

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.