Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton

Word, J. Michael; Lovell, Simon C.; Richardson, Jane S.; Richardson, David C.

doi:10.1006/jmbi.1998.2401

Cited by 1,339 publications

(1,181 citation statements)

References 29 publications

Supporting

Mentioning

1,150

Contrasting

Unclassified

Order By: Relevance

“…The failure of both scoring functions can be attributed to the presence of the metal-ligand interactions in the active site. The Dreiding force field 41 was used for the PDF targets because the CFF 40 did not contain appropriate metal parameters. The poor results obtained here suggest that even the Drieding force field may not adequately handle the metalligand interactions.…”

Section: Resultsmentioning

confidence: 99%

“…The protein atoms were then typed using the CFF force field. 40 In the case of ePDF and sPDF, the binding site nickel ion was not bonded to the amino acid side chains and was typed as a Zn 2+ . The hydrogen positions were energy minimized using either the CFF or the Dreiding force field 41 in the absence of any ligands, while holding the heavy atoms of the protein backbone and side chains fixed.…”

Section: Methodsmentioning

confidence: 99%

“…The ligand database contained cognate ligands for all eight targets and was prepared by adding and deleting hydrogen atoms, consistent with the ionization states of nitrogen and oxygen atoms at physiological pH. Ligand conformations were randomly generated starting from their SMILES strings and energy minimized using the CFF force field 40 and stored in an SD file. The latter was used to generate a database using the CATALYST 42 BEST conformational generation paradigm.…”

Section: Methodsmentioning

confidence: 99%

“…The hydrogen-filled docked poses were minimized in the protein targets using the CFF force field. 40 In the case of enzymes ePDF and sPDF, the Dreiding force field 41 was employed as the CFF lacks suitable parameters for highly coordinated metal ions.…”

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Validation Studies of the Site-Directed Docking Program LibDock

Rao

Head

Kulkarni

et al. 2007

J. Chem. Inf. Model.

297

199

View full text Add to dashboard Cite

The performance of the site-features docking algorithm LibDock has been evaluated across eight GlaxoSmithKline targets as a follow-up to a broad validation study of docking and scoring software (Warren, This study was conducted using DJD scoring, and poses were rescored using all available scoring functions in the Accelrys LigandFit module, including LigScore2. For six out of eight targets at least 30% of the ligands were docked within a root-mean-square difference (RMSD) of 2.0 Å for the crystallographic poses when the LigScore2 scoring function was used. LibDock retrieved at least 20% of active compounds in the top 10% of screened ligands for four of the eight targets in the virtual screening protocol. In both studies the LigScore2 scoring function enhanced the retrieval of crystallographic poses or active compounds in comparison with the results obtained using the DJD scoring function. The results for LibDock accuracy and ligand retrieval in virtual screening are compared to 10 other docking and scoring programs. These studies demonstrate the utility of the LigScore2 scoring function and that LibDock as a feature directed docking method performs as well as docking programs that use genetic/growing and Monte Carlo driven algorithms.G

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Validation Studies of the Site-Directed Docking Program LibDock

Rao

Head

Kulkarni

et al. 2007

J. Chem. Inf. Model.

297

199

View full text Add to dashboard Cite

show abstract

“…42 Crystallization ligands were removed, and two hydroxy bridges between the irons were added to prepare the resting state dihydroxo-diiron(III) form of the enzyme. 42 The protein was protonated using reduce 49 on the basis of PropKa 3.1 results 50 for a pH of 7.8. Considering irons in the +3 oxidation state, the resulting structure had a charge of -15.…”

Section: Computational Detailsmentioning

confidence: 99%

Pathways for Arene Oxidation in Non-Heme Diiron Enzymes: Lessons from Computational Studies on Benzoyl Coenzyme A Epoxidase

Rokob

2016

J. Am. Chem. Soc.

View full text Add to dashboard Cite

Oxygenation of aromatic rings using O2 is catalyzed by several non-heme carboxylate-bridged diiron enzymes. In order to provide a general mechanistic description for these reactions, computational studies were carried out at the ONIOM(B3LYP/BP86/Amber) level on the non-heme diiron enzyme benzoyl Specifically for the BoxB enzyme, the Q pathway was found to be the most preferred, but the corresponding bis(μ-oxo)-diiron(IV) species is significantly destabilized and not expected to be directly observable. Epoxidation via the Pσ* pathway represents an energetically somewhat higher lying alternative; possible strategies for experimental discrimination are discussed. The selectivity toward epoxidation is shown to stem from a combination of inherent electronic properties of the thioacyl substituent and enzymatic constraints. Possible implications of the results for toluene monooxygenases are considered as well.2

show abstract

A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays

Glick

Goldblum

2000

Proteins

View full text Add to dashboard Cite

A novel automated method for the optimal placement of polar hydrogens in a protein structure is presented. The algorithm adds initially, to a protein data bank file of the protein, nonrotatable hydrogens such as peptide backbone hydrogens according to geometric considerations. Then, water protons and polar side chain protons of lysine, serine, threonine, tyrosine, aspartic acid, glutamic acid, and the C and N termini of a protein are added according to energy considerations. A unique stochastic approach has been developed to overcome a combinatorial explosion in the search for the lowest energy structure. First, the system is divided into ensembles. Each ensemble is treated separately: N conformations are sampled at random, their energies computed, whereas common components of high-energy combinations are gathered on one hand, and low-energy combinations on the other. Components that yield only high-energy conformations and do not contribute to any low energies are excluded. This is reiterated while the total amount of combinations is decreased along the iterative process. When the total number of combinations is lower than a user defined threshold, all remaining combinations are evaluated by exhaustive search. Energy evaluations use nonbonding energy expressions alone. The program was tested on five high-resolution crystal structures: bovine pancreatic trypsin inhibitor (Brookhaven Protein Data Bank file 5PTI), RNase-A (5RSA), trypsin (1NTP), and carbon monoxymyoglobin (2MB5), for which neutron diffraction structures are available, as well as phosphate binding protein (1IXH) for which very high resolution X-ray crystallography was used. The low RMS values prove the efficiency of this algorithm as a tool for positioning protons in proteins. It may be used for other biological structures.

show abstract

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton

Cited by 1,339 publications

References 29 publications

Validation Studies of the Site-Directed Docking Program LibDock

Validation Studies of the Site-Directed Docking Program LibDock

Pathways for Arene Oxidation in Non-Heme Diiron Enzymes: Lessons from Computational Studies on Benzoyl Coenzyme A Epoxidase

A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays

Contact Info

Product

Resources

About