Literature DB >> 17642521

ValLigURL: a server for ligand-structure comparison and validation.

Gerard J Kleywegt1, Mark R Harris.   

Abstract

A new web-based tool called ValLigURL is described. It can be used by practising crystallographers to validate the geometry of a ligand and to compare the conformation of a ligand with all instances of that ligand in the structural database (wwPDB). In addition, it can be used by structural bioinformaticians to survey the quality or conformational diversity of any ligand across the entire structural database. The server is freely accessible at the URL http://eds.bmc.uu.se/eds/valligurl.php.

Mesh：

Substances：

Year:  2007        PMID： 17642521     DOI： 10.1107/S090744490703315X

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


  19 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.  PDB ligand conformational energies calculated quantum-mechanically.

Authors:  Markus Sitzmann; Iwona E Weidlich; Igor V Filippov; Chenzhong Liao; Megan L Peach; Wolf-Dietrich Ihlenfeldt; Rajeshri G Karki; Yulia V Borodina; Raul E Cachau; Marc C Nicklaus
Journal:  J Chem Inf Model       Date:  2012-02-21       Impact factor: 4.956

3.  Progress in protein crystallography.

Authors:  Zbigniew Dauter; Alexander Wlodawer
Journal:  Protein Pept Lett       Date:  2016       Impact factor: 1.890

4.  Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.

Authors:  Ivan Shabalin; Zbigniew Dauter; Mariusz Jaskolski; Wladek Minor; Alexander Wlodawer
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-08-28

5.  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

6.  Visualizing ligand molecules in Twilight electron density.

Authors:  Christian X Weichenberger; Edwin Pozharski; Bernhard Rupp
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2013-01-19

7.  X-ray crystallography: Assessment and validation of protein-small molecule complexes for drug discovery.

Authors:  David R Cooper; Przemyslaw J Porebski; Maksymilian Chruszcz; Wladek Minor
Journal:  Expert Opin Drug Discov       Date:  2011-08-01       Impact factor: 6.098

Review 8.  Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.

Authors:  Megan L Peach; Raul E Cachau; Marc C Nicklaus
Journal:  J Mol Recognit       Date:  2017-02-24       Impact factor: 2.137

9.  The structure of myristoylated Mason-Pfizer monkey virus matrix protein and the role of phosphatidylinositol-(4,5)-bisphosphate in its membrane binding.

Authors:  Jan Prchal; Pavel Srb; Eric Hunter; Tomáš Ruml; Richard Hrabal
Journal:  J Mol Biol       Date:  2012-08-02       Impact factor: 5.469

10.  wwLigCSRre: a 3D ligand-based server for hit identification and optimization.

Authors:  O Sperandio; M Petitjean; P Tuffery
Journal:  Nucleic Acids Res       Date:  2009-05-08       Impact factor: 16.971
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.