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

By Nigel W. Moriarty, R. Grosse-Kunstleve, Paul D. Adams. Acta Crystallographica Section D: Biological Crystallography, 2009

530 citations recorded by the source corpus.

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.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Oncology

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Citations in the corpus

The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “The current Phenix release (1.7) includes GUIs for phenix.refine [22], phenix.xtriage , the AutoSol[27], AutoBuild[23], AutoMR, and LigandFit[28, 29] wizards, Phaser[6], eLBOW[30], the restraints editor REEL, validation tools, and utilities for creating and manipulating maps and reflection files.”
Automatically fixing errors in glycoprotein structures with Rosetta (2018, unknown): “To extend Rosetta’s bond geometry term for glycans ideal bond length and bond angles values were taken from phenix using elbow with am1 optimization when the default values in Rosetta were insufﬁcient (Moriarty et al., 2009) and added to the Rosetta database for each glycan in our benchmark set.”
Plasticity in binding confers selectivity in ligand induced protein degradation (2018, unknown): “REFINE 48 and autoBUSTER 49 with ligand restraints generated by Grade server (Global Phasing) or phenix.elbow 50 .”
A New Generation of Crystallographic Validation Tools for the Protein Data Bank (2011, methodology): “Ligand geometry can be optimized with quantum-chemical calculations, as in eLBOW (Moriarty et al., 2009) or by molecular mechanics calculations, as in the PRODRG server (Schu¨ttel-kopf and van Aalten, 2004).”
AceDRG: a stereochemical description generator for ligands (2017, methodology): “There are several good software tools designed for the derivation of accurate values for the bonds and angles in small molecules (Moriarty et al. , 2009; Smart et al. , 2011; Schu¨ttelkopf & van Aalten, 2004).”