Literature DB >> 17989929

Computer-aided drug design: the next 20 years.

John H Van Drie1.   

Abstract

This perspectives article has been taken from a talk the author gave at the symposium in honor of Yvonne C. Martin's retirement, held at the American Chemical Society spring meeting in Chicago on March 25, 2007. The talk was intended as a somewhat lighthearted attempt to gaze into the future; inevitably, in print, things will come across more seriously than was intended. As we all know-the past is rarely predictive of the future.

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Year:  2007        PMID： 17989929     DOI： 10.1007/s10822-007-9142-y

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN： 0920-654X            Impact factor:   3.686


  32 in total

1.  A quantitative analysis of the kinetics of the G(2) DNA damage checkpoint system.

Authors:  B D Aguda
Journal:  Proc Natl Acad Sci U S A       Date:  1999-09-28       Impact factor: 11.205

2.  Activity patterns in a model for the subthalamopallidal network of the basal ganglia.

Authors:  D Terman; J E Rubin; A C Yew; C J Wilson
Journal:  J Neurosci       Date:  2002-04-01       Impact factor: 6.167

3.  Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides.

Authors:  Taha Rezai; Jonathan E Bock; Mai V Zhou; Chakrapani Kalyanaraman; R Scott Lokey; Matthew P Jacobson
Journal:  J Am Chem Soc       Date:  2006-11-01       Impact factor: 15.419

Review 4.  The hypoxic inducible stress response as a target for cancer drug discovery.

Authors:  Sarah J Welsh; Mei Yee Koh; Garth Powis
Journal:  Semin Oncol       Date:  2006-08       Impact factor: 4.929

5.  HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time.

Authors:  A S Perelson; A U Neumann; M Markowitz; J M Leonard; D D Ho
Journal:  Science       Date:  1996-03-15       Impact factor: 47.728

6.  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

7.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

Review 8.  hERG potassium channels and cardiac arrhythmia.

Authors:  Michael C Sanguinetti; Martin Tristani-Firouzi
Journal:  Nature       Date:  2006-03-23       Impact factor: 49.962

9.  Toward a pharmacophore for drugs inducing the long QT syndrome: insights from a CoMFA study of HERG K(+) channel blockers.

Authors:  Andrea Cavalli; Elisabetta Poluzzi; Fabrizio De Ponti; Maurizio Recanatini
Journal:  J Med Chem       Date:  2002-08-29       Impact factor: 7.446

10.  Structures of human MAP kinase kinase 1 (MEK1) and MEK2 describe novel noncompetitive kinase inhibition.

Authors:  Jeffrey F Ohren; Huifen Chen; Alexander Pavlovsky; Christopher Whitehead; Erli Zhang; Peter Kuffa; Chunhong Yan; Patrick McConnell; Cindy Spessard; Craig Banotai; W Thomas Mueller; Amy Delaney; Charles Omer; Judith Sebolt-Leopold; David T Dudley; Iris K Leung; Cathlin Flamme; Joseph Warmus; Michael Kaufman; Stephen Barrett; Haile Tecle; Charles A Hasemann
Journal:  Nat Struct Mol Biol       Date:  2004-11-14       Impact factor: 15.369
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  23 in total

Review 1.  Identification of HIV inhibitors guided by free energy perturbation calculations.

Authors:  Orlando Acevedo; Zandrea Ambrose; Patrick T Flaherty; Hadega Aamer; Prashi Jain; Somisetti V Sambasivarao
Journal:  Curr Pharm Des       Date:  2012       Impact factor: 3.116

Review 2.  Computational methods in drug discovery.

Authors:  Gregory Sliwoski; Sandeepkumar Kothiwale; Jens Meiler; Edward W Lowe
Journal:  Pharmacol Rev       Date:  2013-12-31       Impact factor: 25.468

Review 3.  Biomolecularmodeling and simulation: a field coming of age.

Authors:  Tamar Schlick; Rosana Collepardo-Guevara; Leif Arthur Halvorsen; Segun Jung; Xia Xiao
Journal:  Q Rev Biophys       Date:  2011-05       Impact factor: 5.318

4.  The evolution of drug design at Merck Research Laboratories.

Authors:  Frank K Brown; Edward C Sherer; Scott A Johnson; M Katharine Holloway; Bradley S Sherborne
Journal:  J Comput Aided Mol Des       Date:  2016-11-23       Impact factor: 3.686

5.  A Multimodal Data Analysis Approach for Targeted Drug Discovery Involving Topological Data Analysis (TDA).

Authors:  Muthuraman Alagappan; Dadi Jiang; Nicholas Denko; Albert C Koong
Journal:  Adv Exp Med Biol       Date:  2016       Impact factor: 2.622

6.  Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23.

Authors:  Hector A Velazquez; Demian Riccardi; Zhousheng Xiao; Leigh Darryl Quarles; Charless Ryan Yates; Jerome Baudry; Jeremy C Smith
Journal:  Chem Biol Drug Des       Date:  2017-11-03       Impact factor: 2.817

7.  Computer-Aided Drug Design Methods.

Authors:  Wenbo Yu; Alexander D MacKerell
Journal:  Methods Mol Biol       Date:  2017

8.  Target flexibility: an emerging consideration in drug discovery and design.

Authors:  Pietro Cozzini; Glen E Kellogg; Francesca Spyrakis; Donald J Abraham; Gabriele Costantino; Andrew Emerson; Francesca Fanelli; Holger Gohlke; Leslie A Kuhn; Garrett M Morris; Modesto Orozco; Thelma A Pertinhez; Menico Rizzi; Christoph A Sotriffer
Journal:  J Med Chem       Date:  2008-09-12       Impact factor: 7.446

9.  The future of molecular dynamics simulations in drug discovery.

Authors:  David W Borhani; David E Shaw
Journal:  J Comput Aided Mol Des       Date:  2011-12-20       Impact factor: 3.686

Review 10.  Computer-aided Molecular Design of Compounds Targeting Histone Modifying Enzymes.

Authors:  Federico Andreoli; Alberto Del Rio
Journal:  Comput Struct Biotechnol J       Date:  2015-05-07       Impact factor: 7.271
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