Literature DB >> 19770504

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

Nigel W Moriarty1, Ralf W Grosse-Kunstleve, Paul D Adams.   

Abstract

The electronic Ligand Builder and Optimization Workbench (eLBOW) is a program module of the PHENIX suite of computational crystallographic software. It is designed to be a flexible procedure that uses simple and fast quantum-chemical techniques to provide chemically accurate information for novel and known ligands alike. A variety of input formats and options allow the attainment of a number of diverse goals including geometry optimization and generation of restraints.

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Year:  2009        PMID： 19770504      PMCID： PMC2748967          DOI： 10.1107/S0907444909029436

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


  10 in total

1.  PHENIX: building new software for automated crystallographic structure determination.

Authors:  Paul D Adams; Ralf W Grosse-Kunstleve; Li Wei Hung; Thomas R Ioerger; Airlie J McCoy; Nigel W Moriarty; Randy J Read; James C Sacchettini; Nicholas K Sauter; Thomas C Terwilliger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-10-21

2.  Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

Authors:  Simon C Lovell; Ian W Davis; W Bryan Arendall; Paul I W de Bakker; J Michael Word; Michael G Prisant; Jane S Richardson; David C Richardson
Journal:  Proteins       Date:  2003-02-15

Review 3.  Application and limitations of X-ray crystallographic data in structure-based ligand and drug design.

Authors:  Andrew M Davis; Simon J Teague; Gerard J Kleywegt
Journal:  Angew Chem Int Ed Engl       Date:  2003-06-23       Impact factor: 15.336

Review 4.  Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?

Authors:  Gerard J Kleywegt; Kim Henrick; Eleanor J Dodson; Daan M F van Aalten
Journal:  Structure       Date:  2003-09       Impact factor: 5.006

5.  MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.

Authors:  Ian W Davis; Laura Weston Murray; Jane S Richardson; David C Richardson
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

6.  PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.

Authors:  Alexander W Schüttelkopf; Daan M F van Aalten
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-07-21

7.  Optimization of parameters for semiempirical methods IV: extension of MNDO, AM1, and PM3 to more main group elements.

Authors:  James J P Stewart
Journal:  J Mol Model       Date:  2004-03-02       Impact factor: 1.810

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

Authors:  S Wlodek; A G Skillman; A Nicholls
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-06-20

9.  RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I.

Authors:  Gerd B Rocha; Ricardo O Freire; Alfredo M Simas; James J P Stewart
Journal:  J Comput Chem       Date:  2006-07-30       Impact factor: 3.376

10.  A robust bulk-solvent correction and anisotropic scaling procedure.

Authors:  Pavel V Afonine; Ralf W Grosse-Kunstleve; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-06-24
  10 in total
  446 in total

1.  Joint X-ray and neutron refinement with phenix.refine.

Authors:  Pavel V Afonine; Marat Mustyakimov; Ralf W Grosse-Kunstleve; Nigel W Moriarty; Paul Langan; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-10-20

2.  Structural basis for antiviral inhibition of the main protease, 3C, from human enterovirus 93.

Authors:  Lionel Costenaro; Zuzanna Kaczmarska; Carme Arnan; Robert Janowski; Bruno Coutard; Maria Solà; Alexander E Gorbalenya; Heléne Norder; Bruno Canard; Miquel Coll
Journal:  J Virol       Date:  2011-08-10       Impact factor: 5.103

3.  The Gal3p transducer of the GAL regulon interacts with the Gal80p repressor in its ligand-induced closed conformation.

Authors:  Tali Lavy; P Rajesh Kumar; Hongzhen He; Leemor Joshua-Tor
Journal:  Genes Dev       Date:  2012-02-01       Impact factor: 11.361

4.  Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member.

Authors:  Huei-Jiun Li; Xiaokai Li; Nina Liu; Huaning Zhang; James J Truglio; Shambhavi Mishra; Caroline Kisker; Miguel Garcia-Diaz; Peter J Tonge
Journal:  Biochemistry       Date:  2011-10-11       Impact factor: 3.162

5.  Structure-based drug design and optimization of mannoside bacterial FimH antagonists.

Authors:  Zhenfu Han; Jerome S Pinkner; Bradley Ford; Robert Obermann; William Nolan; Scott A Wildman; Doug Hobbs; Tom Ellenberger; Corinne K Cusumano; Scott J Hultgren; James W Janetka
Journal:  J Med Chem       Date:  2010-06-24       Impact factor: 7.446

6.  Structural Basis for Substrate Specificity in Adenosylcobalamin-dependent Isobutyryl-CoA Mutase and Related Acyl-CoA Mutases.

Authors:  Marco Jost; David A Born; Valentin Cracan; Ruma Banerjee; Catherine L Drennan
Journal:  J Biol Chem       Date:  2015-08-28       Impact factor: 5.157

7.  Structural Insights into Anthranilate Priming during Type II Polyketide Biosynthesis.

Authors:  David R Jackson; Stephanie S Tu; MyChi Nguyen; Jesus F Barajas; Andrew J Schaub; Daniel Krug; Dominik Pistorius; Ray Luo; Rolf Müller; Shiou-Chuan Tsai
Journal:  ACS Chem Biol       Date:  2015-11-03       Impact factor: 5.100

8.  An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography.

Authors:  Agata Butryn; Philipp S Simon; Pierre Aller; Philip Hinchliffe; Ramzi N Massad; Gabriel Leen; Catherine L Tooke; Isabel Bogacz; In-Sik Kim; Asmit Bhowmick; Aaron S Brewster; Nicholas E Devenish; Jürgen Brem; Jos J A G Kamps; Pauline A Lang; Patrick Rabe; Danny Axford; John H Beale; Bradley Davy; Ali Ebrahim; Julien Orlans; Selina L S Storm; Tiankun Zhou; Shigeki Owada; Rie Tanaka; Kensuke Tono; Gwyndaf Evans; Robin L Owen; Frances A Houle; Nicholas K Sauter; Christopher J Schofield; James Spencer; Vittal K Yachandra; Junko Yano; Jan F Kern; Allen M Orville
Journal:  Nat Commun       Date:  2021-07-22       Impact factor: 14.919

9.  Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution.

Authors:  Sibel Kalyoncu; David P Heaner; Raquel L Lieberman; Zohre Kurt; Casey M Bethel; Chiamaka U Ukachukwu; Srinivas Chakravarthy; Jim C Spain
Journal:  Nat Chem Biol       Date:  2016-10-03       Impact factor: 15.040

10.  Chemically Linked Vemurafenib Inhibitors Promote an Inactive BRAFV600E Conformation.

Authors:  Michael Grasso; Michelle A Estrada; Christian Ventocilla; Minu Samanta; Jasna Maksimoska; Jessie Villanueva; Jeffrey D Winkler; Ronen Marmorstein
Journal:  ACS Chem Biol       Date:  2016-09-06       Impact factor: 5.100
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