Name: Enlighten2 PyMOL plugin c Date: 2020-10-15 00:00:00 UTC
Description: The Enlighten2 PyMOL plugin code can be downloaded directly from the project website (https://en...
DOI:
Location: https://enlighten2.github.io/
Article: Enlighten2: molecular dynamics simulations of protein–ligand systems made accessible
|
Name: Narupa 2 Protocol Date: 2022-04-25 00:00:00 UTC
Description: The programs necessary for running a standalone simulation of trypsin and benzamidine in Narupa ...
DOI:
Location: https://gitlab.com/intangiblerealities/narupa-protocol
Article: Free energy along drug-protein binding pathways interactively sampled in virtual reality
|
Name: PDB Entry - 6TAE Date: 2020-04-08 00:00:00 UTC
Description: PDB Entry - 6TAE Neutron structure of ferric ascorbate peroxidase
DOI: 10.2210/pdb6tae/pdb
Location: https://www.wwpdb.org/pdb?id=pdb_00006TAE http://www.ebi.ac.uk/pdbe-srv/view/entry/6tae https://www.rcsb.org/structure/6TAE
Article: Visualizing the protons in a metalloenzyme electron proton transfer pathway
|
Name: PDB Entry - 6XV4 Date: 2020-04-08 00:00:00 UTC
Description: PDB Entry - 6XV4 Neutron structure of ferric ascorbate peroxidase-ascorbate complex
DOI: 10.2210/pdb6xv4/pdb
Location: https://www.wwpdb.org/pdb?id=pdb_00006XV4 http://www.ebi.ac.uk/pdbe-srv/view/entry/6xv4 https://www.rcsb.org/structure/6XV4
Article: Visualizing the protons in a metalloenzyme electron proton transfer pathway
|
Name: PDB Entry - 7QVH The crystal structure of HotPETase, an evolved thermostable variant of IsPETase Date: 2023-02-15 00:00:00 UTC
Description: PDB Entry - 7QVH(Status - Released) summary information: Title: The crystal structure of HotPETa...
DOI: 10.2210/pdb7qvh/pdb
Location: https://www.wwpdb.org/pdb?id=pdb_00007qvh http://www.ebi.ac.uk/pdbe-srv/view/entry/7qvh https://www.rcsb.org/structure/7QVH
Article: Directed evolution of an efficient and thermostable PET depolymerase
|
Name: Supplemental Information 1: Molecular xyz coordinates Date: 2020-05-20 00:00:00 UTC
Description: Related Article: Sirirak, Jitnapa, Lawan, Narin, Van der Kamp, Marc W., Harvey, Jeremy N., Mulho...
DOI: 10.7717/peerj-pchem.8/supp-1
Location: http://dx.doi.org/10.7717/peerj-pchem.8/supp-1
Article: Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes
|
Name: Table S1: Coordinates of 29 molecules optimized at the B3LYP/6-311+G(d) level Date: 2020-05-20 00:00:00 UTC
Description: Related Article: Sirirak, Jitnapa, Lawan, Narin, Van der Kamp, Marc W., Harvey, Jeremy N., Mulho...
DOI: 10.7717/peerj-pchem.8/supp-2
Location: http://dx.doi.org/10.7717/peerj-pchem.8/supp-2
Article: Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes
|
Name: Table S2: Molecular energies of molecular No.1 (M1) to molecular No.29 (M29) (in kcal mol−1) calculated by 24 QM methods using the structure optimized at the B3LYP/6-311+G(d) level as starting structures Date: 2020-05-20 00:00:00 UTC
Description: Related Article: Sirirak, Jitnapa, Lawan, Narin, Van der Kamp, Marc W., Harvey, Jeremy N., Mulho...
DOI: 10.7717/peerj-pchem.8/supp-3
Location: http://dx.doi.org/10.7717/peerj-pchem.8/supp-3
Article: Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes
|
Name: Table S3: Reaction energies (in kcal mol−1) of reaction 1–20 calculated by 24 quantum mechanics methods Date: 2020-05-20 00:00:00 UTC
Description: Related Article: Sirirak, Jitnapa, Lawan, Narin, Van der Kamp, Marc W., Harvey, Jeremy N., Mulho...
DOI: 10.7717/peerj-pchem.8/supp-4
Location: http://dx.doi.org/10.7717/peerj-pchem.8/supp-4
Article: Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes
|
Name: Table S4: Errors of reaction energies (in kcal mol−1) of reaction 1–20, relative to the CCSD(T)/aug-cc-pVTZ results Date: 2020-05-20 00:00:00 UTC
Description: Related Article: Sirirak, Jitnapa, Lawan, Narin, Van der Kamp, Marc W., Harvey, Jeremy N., Mulho...
DOI: 10.7717/peerj-pchem.8/supp-5
Location: http://dx.doi.org/10.7717/peerj-pchem.8/supp-5
Article: Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes
|