Literature DB >> 21707404

Software and resources for computational medicinal chemistry.

Chenzhong Liao1, Markus Sitzmann, Angelo Pugliese, Marc C Nicklaus.   

Abstract

Computer-aided drug design plays a vital role in drug discovery and development and has become an indispensable tool in the pharmaceutical industry. Computational medicinal chemists can take advantage of all kinds of software and resources in the computer-aided drug design field for the purposes of discovering and optimizing biologically active compounds. This article reviews software and other resources related to computer-aided drug design approaches, putting particular emphasis on structure-based drug design, ligand-based drug design, chemical databases and chemoinformatics tools.

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Year:  2011        PMID: 21707404      PMCID: PMC3413324          DOI: 10.4155/fmc.11.63

Source DB:  PubMed          Journal:  Future Med Chem        ISSN: 1756-8919            Impact factor:   3.808


  144 in total

1.  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

2.  Design, synthesis and evaluation of 5-substituted amino-2,4-diamino-8-chloropyrimido-[4,5-b]quinolines as novel antimalarials.

Authors:  Advait A Joshi; Sachin S Narkhede; C L Viswanathan
Journal:  Bioorg Med Chem Lett       Date:  2005-01-03       Impact factor: 2.823

3.  The GROMOS software for biomolecular simulation: GROMOS05.

Authors:  Markus Christen; Philippe H Hünenberger; Dirk Bakowies; Riccardo Baron; Roland Bürgi; Daan P Geerke; Tim N Heinz; Mika A Kastenholz; Vincent Kräutler; Chris Oostenbrink; Christine Peter; Daniel Trzesniak; Wilfred F van Gunsteren
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

Review 4.  Molecule-pharmacophore superpositioning and pattern matching in computational drug design.

Authors:  Gerhard Wolber; Thomas Seidel; Fabian Bendix; Thierry Langer
Journal:  Drug Discov Today       Date:  2007-11-05       Impact factor: 7.851

5.  Virtual screening approach for the identification of new Rac1 inhibitors.

Authors:  Nicola Ferri; Alberto Corsini; Paolo Bottino; Francesca Clerici; Alessandro Contini
Journal:  J Med Chem       Date:  2009-07-23       Impact factor: 7.446

6.  Identification of novel cannabinoid CB1 receptor antagonists by using virtual screening with a pharmacophore model.

Authors:  Hongwu Wang; Ruth A Duffy; George C Boykow; Samuel Chackalamannil; Vincent S Madison
Journal:  J Med Chem       Date:  2008-03-26       Impact factor: 7.446

Review 7.  Three-dimensional pharmacophore methods in drug discovery.

Authors:  Andrew R Leach; Valerie J Gillet; Richard A Lewis; Robin Taylor
Journal:  J Med Chem       Date:  2010-01-28       Impact factor: 7.446

8.  Exploring Potential Binding Modes of Small Drug-like Molecules to the Polo-Box Domain of Human Polo-like Kinase 1.

Authors:  Chenzhong Liao; Jung-Eun Park; Jeong Kyu Bang; Marc C Nicklaus; Kyung S Lee
Journal:  ACS Med Chem Lett       Date:  2010       Impact factor: 4.345

9.  Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity.

Authors:  G Klebe; U Abraham; T Mietzner
Journal:  J Med Chem       Date:  1994-11-25       Impact factor: 7.446

10.  Selection of evodiamine as a novel topoisomerase I inhibitor by structure-based virtual screening and hit optimization of evodiamine derivatives as antitumor agents.

Authors:  Guoqiang Dong; Chunquan Sheng; Shengzheng Wang; Zhenyuan Miao; Jianzhong Yao; Wannian Zhang
Journal:  J Med Chem       Date:  2010-11-11       Impact factor: 7.446

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  24 in total

1.  Identification of hub genes related to the progression of type 1 diabetes by computational analysis.

Authors:  G Prashanth; Basavaraj Vastrad; Anandkumar Tengli; Chanabasayya Vastrad; Iranna Kotturshetti
Journal:  BMC Endocr Disord       Date:  2021-04-07       Impact factor: 2.763

2.  Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics.

Authors:  Andrey V Ilatovskiy; Ruben Abagyan; Irina Kufareva
Journal:  Int J Quantum Chem       Date:  2013-06-15       Impact factor: 2.444

3.  Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

Authors:  Juyong Lee; Florentina Tofoleanu; Frank C Pickard; Gerhard König; Jing Huang; Ana Damjanović; Minkyung Baek; Chaok Seok; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-09-27       Impact factor: 3.686

4.  Discovery and identification of PIM-1 kinase inhibitors through a hybrid screening approach.

Authors:  Mingfeng Shao; Yiming Yuan; Kun Yu; Kai Lei; Guonian Zhu; Lijuan Chen; Mingli Xiang
Journal:  Mol Divers       Date:  2014-02-12       Impact factor: 2.943

5.  Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations.

Authors:  Hugo Guterres; Wonpil Im
Journal:  J Chem Inf Model       Date:  2020-04-10       Impact factor: 4.956

6.  D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Authors:  Conor D Parks; Zied Gaieb; Michael Chiu; Huanwang Yang; Chenghua Shao; W Patrick Walters; Johanna M Jansen; Georgia McGaughey; Richard A Lewis; Scott D Bembenek; Michael K Ameriks; Tara Mirzadegan; Stephen K Burley; Rommie E Amaro; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2020-01-23       Impact factor: 3.686

Review 7.  Modern approaches to accelerate discovery of new antischistosomal drugs.

Authors:  Bruno Junior Neves; Eugene Muratov; Renato Beilner Machado; Carolina Horta Andrade; Pedro Vitor Lemos Cravo
Journal:  Expert Opin Drug Discov       Date:  2016-05-03       Impact factor: 6.098

Review 8.  Chemical screening in zebrafish for novel biological and therapeutic discovery.

Authors:  D S Wiley; S E Redfield; L I Zon
Journal:  Methods Cell Biol       Date:  2016-12-29       Impact factor: 1.441

9.  ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.

Authors:  Janez Konc; Tomo Cesnik; Joanna Trykowska Konc; Matej Penca; Dušanka Janežič
Journal:  J Chem Inf Model       Date:  2012-02-07       Impact factor: 4.956

10.  Identification of candidate biomarkers and therapeutic agents for heart failure by bioinformatics analysis.

Authors:  Vijayakrishna Kolur; Basavaraj Vastrad; Chanabasayya Vastrad; Shivakumar Kotturshetti; Anandkumar Tengli
Journal:  BMC Cardiovasc Disord       Date:  2021-07-04       Impact factor: 2.298

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