Literature DB >> 20349528

Novel opportunities for computational biology and sociology in drug discovery.

Lixia Yao1, James A Evans, Andrey Rzhetsky.   

Abstract

Current drug discovery is impossible without sophisticated modeling and computation. In this review we outline previous advances in computational biology and, by tracing the steps involved in pharmaceutical development,explore a range of novel, high-value opportunities for computational innovation in modeling the biological process of disease and the social process of drug discovery.These opportunities include text mining for new drug leads, modeling molecular pathways and predicting the efficacy of drug cocktails, analyzing genetic overlap between diseases and predicting alternative drug use.Computation can also be used to model research teams and innovative regions and to estimate the value of academy-industry links for scientific and human benefit. Attention to these opportunities could promise punctuated advance and will complement the well-established computational work on which drug discovery currently relies.

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Year:  2010        PMID: 20349528      PMCID: PMC3654551          DOI: 10.1016/j.tibtech.2010.01.004

Source DB:  PubMed          Journal:  Trends Biotechnol        ISSN: 0167-7799            Impact factor:   19.536


  49 in total

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Authors:  Gordana Apic; Tijana Ignjatovic; Scott Boyer; Robert B Russell
Journal:  FEBS Lett       Date:  2005-03-21       Impact factor: 4.124

Review 2.  Erythropoietin after a century of research: younger than ever.

Authors:  Wolfgang Jelkmann
Journal:  Eur J Haematol       Date:  2007-01-23       Impact factor: 2.997

3.  Quantitative systems-level determinants of human genes targeted by successful drugs.

Authors:  Lixia Yao; Andrey Rzhetsky
Journal:  Genome Res       Date:  2007-12-14       Impact factor: 9.043

4.  Structural diversity of organic chemistry. A scaffold analysis of the CAS Registry.

Authors:  Alan H Lipkus; Qiong Yuan; Karen A Lucas; Susan A Funk; William F Bartelt; Roger J Schenck; Anthony J Trippe
Journal:  J Org Chem       Date:  2008-05-28       Impact factor: 4.354

5.  Drug-target network.

Authors:  Muhammed A Yildirim; Kwang-Il Goh; Michael E Cusick; Albert-László Barabási; Marc Vidal
Journal:  Nat Biotechnol       Date:  2007-10       Impact factor: 54.908

6.  Treatment of anxiety using fenobam (a nonbenzodiazepine) in a double-blind standard (diazepam) placebo-controlled study.

Authors:  J C Pecknold; D J McClure; L Appeltauer; L Wrzesinski; T Allan
Journal:  J Clin Psychopharmacol       Date:  1982-04       Impact factor: 3.153

7.  Failure of serum transforming growth factor-beta (TGF-beta1) as a biomarker of radiographic osteoarthritis at the knee and hip: a cross-sectional analysis in the Johnston County Osteoarthritis Project.

Authors:  A E Nelson; F Fang; X A Shi; V B Kraus; T Stabler; J B Renner; T A Schwartz; C G Helmick; J M Jordan
Journal:  Osteoarthritis Cartilage       Date:  2008-11-21       Impact factor: 6.576

8.  Computational analysis of the synergy among multiple interacting genes.

Authors:  Dimitris Anastassiou
Journal:  Mol Syst Biol       Date:  2007-02-13       Impact factor: 11.429

Review 9.  Novel statistical tools for monitoring the safety of marketed drugs.

Authors:  J S Almenoff; E N Pattishall; T G Gibbs; W DuMouchel; S J W Evans; N Yuen
Journal:  Clin Pharmacol Ther       Date:  2007-05-30       Impact factor: 6.875

10.  Harnessing naturally randomized transcription to infer regulatory relationships among genes.

Authors:  Lin S Chen; Frank Emmert-Streib; John D Storey
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

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  10 in total

1.  A correlation study of biological activity and molecular docking of Asp and Glu linked bis-hydrazones of quinazolinones.

Authors:  H K Kumara; R Suhas; D M Suyoga Vardhan; M Shobha; D Channe Gowda
Journal:  RSC Adv       Date:  2018-03-16       Impact factor: 4.036

2.  Identification of novel immune-relevant drug target genes for Alzheimer's Disease by combining ontology inference with network analysis.

Authors:  Zhi-Jie Han; Wei-Wei Xue; Lin Tao; Feng Zhu
Journal:  CNS Neurosci Ther       Date:  2018-08-14       Impact factor: 5.243

3.  Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics.

Authors:  Bhanwar Lal Puniya; Laura Allen; Colleen Hochfelder; Mahbubul Majumder; Tomáš Helikar
Journal:  Front Bioeng Biotechnol       Date:  2016-02-11

4.  A comparative chemogenic analysis for predicting Drug-Target Pair via Machine Learning Approaches.

Authors:  Aman Chandra Kaushik; Aamir Mehmood; Xiaofeng Dai; Dong-Qing Wei
Journal:  Sci Rep       Date:  2020-04-22       Impact factor: 4.379

5.  Predicting drug-target interactions from drug structure and protein sequence using novel convolutional neural networks.

Authors:  ShanShan Hu; Chenglin Zhang; Peng Chen; Pengying Gu; Jun Zhang; Bing Wang
Journal:  BMC Bioinformatics       Date:  2019-12-24       Impact factor: 3.169

6.  Novel drug-target interactions via link prediction and network embedding.

Authors:  E Amiri Souri; R Laddach; S N Karagiannis; L G Papageorgiou; S Tsoka
Journal:  BMC Bioinformatics       Date:  2022-04-04       Impact factor: 3.169

7.  A geometric deep learning model for display and prediction of potential drug-virus interactions against SARS-CoV-2.

Authors:  Bihter Das; Mucahit Kutsal; Resul Das
Journal:  Chemometr Intell Lab Syst       Date:  2022-08-24       Impact factor: 4.175

8.  Chemical named entity recognition in the texts of scientific publications using the naïve Bayes classifier approach.

Authors:  O A Tarasova; A V Rudik; N Yu Biziukova; D A Filimonov; V V Poroikov
Journal:  J Cheminform       Date:  2022-08-13       Impact factor: 8.489

9.  Genome-scale screening of drug-target associations relevant to Ki using a chemogenomics approach.

Authors:  Dong-Sheng Cao; Yi-Zeng Liang; Zhe Deng; Qian-Nan Hu; Min He; Qing-Song Xu; Guang-Hua Zhou; Liu-Xia Zhang; Zi-xin Deng; Shao Liu
Journal:  PLoS One       Date:  2013-04-05       Impact factor: 3.240

Review 10.  Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity.

Authors:  C Anthony Hunt; Ryan C Kennedy; Sean H J Kim; Glen E P Ropella
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2013-06-04
  10 in total

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