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
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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
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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
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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
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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
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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
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Name: Table S5: Mean signed errors, standard deviations, maximum errors and minimum errors along with their reaction number (Rxn No.) of reaction energies (in kcal mol<sup>−1</sup>) of reaction 1–20 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-6
Location: http://dx.doi.org/10.7717/peerj-pchem.8/supp-6
Article: Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes
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Name: Table S6: Absolute errors, mean absolute errors and standard deviations of reaction energies (in kcal mol−1) of reaction 1–20. The absolute errors are given 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-7
Location: http://dx.doi.org/10.7717/peerj-pchem.8/supp-7
Article: Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes
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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
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