Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.

By J. Word, S. Lovell, Jane S. Richardson, David C Richardson. 1999

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Citations in the corpus

Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013, methodology): “Hydrogen atom coordinates were optimized using Reduce (Word, Lovell, Richardson, & Richardson, 1999).”
Ligand Pose and Orientational Sampling in Molecular Docking (2013, methodology): “Previous methods for protonation of sidechains have been replaced with REDUCE[121] as it was the most adaptable program, capable of protonating only sidechains that are requested and to not move heavy atoms during the protonation procedure.”
Computer-Aided Drug Design Methods (2017, background): “Software such as Reduce (63) can be used for this purpose.”
Joint X-ray and neutron refinement with phenix.refine. (2010, methodology): “H or D atoms can be added to the model using the phenix.ready_set command-line tool that internally uses the REDUCE (Word et al., 1999) and eLBOW (Moriarty et al., 2009) programs.”
Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures (2017, methodology): “Some tools are available that aid in this understanding, such as the Ligand Protein Contacts server [10] and GIANT [9], and specific programs for ight © 2016 Published by Elsevier Ltd. rg/licenses/by/4.0/). calculating individual interaction types such as polar contacts in PyMOL and hydrogen bonds w”
An efficient algorithm for multistate protein design based on FASTER (2009, methodology): “Hydrogens were removed from each ensemble member and added back in optimized positions using REDUCE.(27) Each structure was then standardized via 50 steps of conjugate-gradient minimization with the DREIDING force field.”
An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling (2011, methodology): “The Rosetta packer algorithm (2, 3) originally written for protein side-chain packing and design, was used to determine the optimal orientation of these 2 ́-OH hydrogen atoms in all loop nucleotides as well as in all surrounding nucleotides through efficient combinatorial sampling, similar to REDUCE”
SHIFTX2: significantly improved protein chemical shift prediction (2011, methodology): “H atoms added) using the program called REDUCE (Word et al. 1999).”
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes (2004, background): “All hydrogen atoms, both polar and nonpolar, are added by the REDUCE program (10).”