Literature DB >> 16790930

Automated ligand placement and refinement with a combined force field and shape potential.

S Wlodek1, A G Skillman, A Nicholls.   

Abstract

An automated computational procedure for fitting a ligand into its electron density with the use of the MMFF94 force field and a Gaussian shape description has been developed. It employs a series of adiabatic optimizations of gradually increasing shape potential. Starting from a set of energy-relaxed ligand conformations, the final results are structures realistically strained to fit the crystallographic data.

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Year:  2006        PMID： 16790930     DOI： 10.1107/S0907444906016076

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN： 0907-4449


  37 in total

1.  Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes.

Authors:  Alpeshkumar K Malde; Alan E Mark
Journal:  J Comput Aided Mol Des       Date:  2010-11-04       Impact factor: 3.686

2.  Models of protein-ligand crystal structures: trust, but verify.

Authors:  Marc C Deller; Bernhard Rupp
Journal:  J Comput Aided Mol Des       Date:  2015-02-10       Impact factor: 3.686

3.  electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation.

Authors:  Nigel W Moriarty; Ralf W Grosse-Kunstleve; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-09-16

4.  Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations.

Authors:  Nathan M Lim; Meghan Osato; Gregory L Warren; David L Mobley
Journal:  J Chem Theory Comput       Date:  2020-03-27       Impact factor: 6.006

5.  The SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity.

Authors:  Kenneth D Bromberg; Taylor R H Mitchell; Anup K Upadhyay; Clarissa G Jakob; Manisha A Jhala; Kenneth M Comess; Loren M Lasko; Conglei Li; Creighton T Tuzon; Yujia Dai; Fengling Li; Mohammad S Eram; Alexander Nuber; Niru B Soni; Vlasios Manaves; Mikkel A Algire; Ramzi F Sweis; Maricel Torrent; Gunnar Schotta; Chaohong Sun; Michael R Michaelides; Alex R Shoemaker; Cheryl H Arrowsmith; Peter J Brown; Vijayaratnam Santhakumar; Alberto Martin; Judd C Rice; Gary G Chiang; Masoud Vedadi; Dalia Barsyte-Lovejoy; William N Pappano
Journal:  Nat Chem Biol       Date:  2017-01-23       Impact factor: 15.040

6.  Fragmentation-tree density representation for crystallographic modelling of bound ligands.

Authors:  Gerrit G Langer; Guillaume X Evrard; Ciaran G Carolan; Victor S Lamzin
Journal:  J Mol Biol       Date:  2012-03-23       Impact factor: 5.469

7.  Protein-ligand cocrystal structures: we can do better.

Authors:  Charles H Reynolds
Journal:  ACS Med Chem Lett       Date:  2014-06-02       Impact factor: 4.345

8.  Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

Authors:  Oleg Y Borbulevych; Joshua A Plumley; Roger I Martin; Kenneth M Merz; Lance M Westerhoff
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-04-26

9.  Conformational analysis and parallel QM/MM X-ray refinement of protein bound anti-Alzheimer drug donepezil.

Authors:  Zheng Fu; Xue Li; Yipu Miao; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2013-02-18       Impact factor: 6.006

10.  Molecular shape and medicinal chemistry: a perspective.

Authors:  Anthony Nicholls; Georgia B McGaughey; Robert P Sheridan; Andrew C Good; Gregory Warren; Magali Mathieu; Steven W Muchmore; Scott P Brown; J Andrew Grant; James A Haigh; Neysa Nevins; Ajay N Jain; Brian Kelley
Journal:  J Med Chem       Date:  2010-05-27       Impact factor: 7.446
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