Predicted relative MM-GBSA free energies (kcal/mol) and individual energy terms of the complexes between shorter chain peptides derived from Kemptide and PKA.

Computing free energies of protein-ligand association

Donnini, S. (Serena)

October 2007

Abstract Spontaneous changes in protein systems, such as the binding of a ligand to an enzyme or rec...

Binding Free-Energy Calculation Is a Powerful Tool for Drug Optimization: Calculation and Measurement of Binding Free Energy for 7‑Azaindole Derivatives to Glycogen Synthase Kinase-3β

Kunihiro Kitamura (1681630)
Yunoshin Tamura (1788742)
Tomokazu Ueki (1788739)
Koji Ogata (494313)
Shigeho Noda (1788745)
Ryutaro Himeno (77159)
Hiroshi Chuman (1788748)

June 2014

Present computational lead (drug)-optimization is lacking in thermodynamic tactics. To examine wheth...

FSH/FSHR binding free energies as computed from GBSA molecular dynamics studies.

Biswa Ranjan Meher (473112)
Anshuman Dixit (163621)
George R. Bousfield (799711)
Gerald H. Lushington (799712)

September 2015

Values are in kcal/mol. Parenthetical values represent standard deviations in the free energies.<...

Predicted relative MM-GBSA free energies (kcal/mol) and individual energy terms of the complexes between mutant peptides derived from Kemptide and PKA.

Karel Mena-Ulecia (596272)
Ariela Vergara-Jaque (638616)
Horacio Poblete (638617)
William Tiznado (596273)
Julio Caballero (531146)

October 2014

a Calculated binding energies do not include entropy term.Predicted relative MM-GBSA free ...

Predicted MM-GBSA free energies (kcal/mol) and individual energy terms of the thrombin-inhibitor complexes for selected compounds.

Karel Mena-Ulecia (596272)
William Tiznado (596273)
Julio Caballero (531146)

November 2015

a Experimental ΔΔG was calculated using ΔG of compound 133 as reference.Predicted M...

Binding free energies calculated by MM-GBSA method (kcal·mol−1).

Shuhua Shi (418270)
Shaolong Zhang (819760)
Qinggang Zhang (819761)

October 2015

Binding free energies calculated by MM-GBSA method (kcal·mol−1).</p

Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK.

Kasper, P
Christen, P
Gehring, H

August 2000

We describe a methodology to calculate the relative free energies of protein-peptide complex formati...

Study of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSA.

Karel Mena-Ulecia
Ariela Vergara-Jaque
Horacio Poblete
William Tiznado
Julio Caballero

We have carried out a protocol in computational biochemistry including molecular dynamics (MD) simul...

The MM-GBSA binding free energies (kcal/mol) of three different VDR and CYP24A1 models.

Selvaraman Nagamani (819665)
Karthikeyan Muthusamy (819667)

October 2018

The MM-GBSA binding free energies (kcal/mol) of three different VDR and CYP24A1 models.</p

Binding free energy predicted using MM/PBSA calculation for 18, 21 and panduratin A.

Maywan Hariono (6260969)
Sy Bing Choi (4408978)
Ros Fatihah Roslim (6260972)
Mohamed Sufian Nawi (6260975)
Mei Lan Tan (678491)
Ezatul Ezleen Kamarulzaman (6260978)
Nornisah Mohamed (1375221)
Rohana Yusof (401395)
Shatrah Othman (6260981)
Noorsaadah Abd Rahman (550281)
Rozana Othman (677989)
Habibah A. Wahab (1425556)

January 2019

Binding free energy predicted using MM/PBSA calculation for 18, 21 and panduratin A.</p

Binding free energies calculations for peptide-MHC complexes.

Amit Kumar (81180)
Eleonora Cocco (314181)
Luigi Atzori (394676)
Maria Giovanna Marrosu (314216)
Enrico Pieroni (326611)

March 2013

Predisposing (*15:01) and protective (*16:01) alleles bound to MBP and EBNA-1. In column 2 is rep...

Study of the Affinity between the Protein Kinase PKA and Peptide Substrates Derived from Kemptide Using Molecular Dynamics Simulations and MM/GBSA

Mena-Ulecia, K.
Vergara-Jaque, A.
Poblete, H.
Tiznado, W.
Caballero, J.

October 2014

Vergara-Jaque, A (Vergara-Jaque, Ariela); Poblete, H (Poblete, Horacio); Caballero, J (Caballero, Ju...

Hydrogen-Bond occupancies analysis from the results of MD simulations for the peptide-PKA interactions for shorter chain peptides derived from Kemptide (WT).

Karel Mena-Ulecia (596272)
Ariela Vergara-Jaque (638616)
Horacio Poblete (638617)
William Tiznado (596273)
Julio Caballero (531146)

October 2014

a Peptide-PKA heavy atoms that form a HB (Notations of atoms refer to the name of atoms from the ...

Contribution of the interactions energy in kcal/mol of the PspA binding residues in the 3 Å from peptides.

Hassan Mahmood Jindal (750256)
Cheng Foh Le (750257)
Mohd Yasim Mohd Yusof (220988)
Rukumani Devi Velayuthan (750258)
Vannajan Sanghiran Lee (750259)
Sharifuddin Md Zain (750260)
Diyana Mohd Isa (750261)
Shamala Devi Sekaran (165904)

June 2015

Contribution of the interactions energy in kcal/mol of the PspA binding residues in the 3 Å from ...

Total binding free energies of WT-EGFR and EGFRL858R in complex to MIG6-YY, Peptides 5, 6, 10, 26 and 27 obtained by MM-PBSA method.

Farial Tavakoli (6725735)
Mohamad Reza Ganjalikhany (153022)

May 2019

Total binding free energies of WT-EGFR and EGFRL858R in complex to MIG6-YY, Peptides 5, 6, 10, 26 an...

Computing free energies of protein-ligand association

Donnini, S. (Serena)

October 2007

Abstract Spontaneous changes in protein systems, such as the binding of a ligand to an enzyme or rec...

Binding Free-Energy Calculation Is a Powerful Tool for Drug Optimization: Calculation and Measurement of Binding Free Energy for 7‑Azaindole Derivatives to Glycogen Synthase Kinase-3β

Kunihiro Kitamura (1681630)
Yunoshin Tamura (1788742)
Tomokazu Ueki (1788739)
Koji Ogata (494313)
Shigeho Noda (1788745)
Ryutaro Himeno (77159)
Hiroshi Chuman (1788748)

June 2014

Present computational lead (drug)-optimization is lacking in thermodynamic tactics. To examine wheth...

FSH/FSHR binding free energies as computed from GBSA molecular dynamics studies.

Biswa Ranjan Meher (473112)
Anshuman Dixit (163621)
George R. Bousfield (799711)
Gerald H. Lushington (799712)

September 2015

Values are in kcal/mol. Parenthetical values represent standard deviations in the free energies.<...

Predicted relative MM-GBSA free energies (kcal/mol) and individual energy terms of the complexes between mutant peptides derived from Kemptide and PKA.

Karel Mena-Ulecia (596272)
Ariela Vergara-Jaque (638616)
Horacio Poblete (638617)
William Tiznado (596273)
Julio Caballero (531146)

October 2014

a Calculated binding energies do not include entropy term.Predicted relative MM-GBSA free ...

Predicted MM-GBSA free energies (kcal/mol) and individual energy terms of the thrombin-inhibitor complexes for selected compounds.

Karel Mena-Ulecia (596272)
William Tiznado (596273)
Julio Caballero (531146)

November 2015

a Experimental ΔΔG was calculated using ΔG of compound 133 as reference.Predicted M...

Binding free energies calculated by MM-GBSA method (kcal·mol−1).

Shuhua Shi (418270)
Shaolong Zhang (819760)
Qinggang Zhang (819761)

October 2015

Binding free energies calculated by MM-GBSA method (kcal·mol−1).</p

Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK.

Kasper, P
Christen, P
Gehring, H

August 2000

We describe a methodology to calculate the relative free energies of protein-peptide complex formati...

Study of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSA.

Karel Mena-Ulecia
Ariela Vergara-Jaque
Horacio Poblete
William Tiznado
Julio Caballero

We have carried out a protocol in computational biochemistry including molecular dynamics (MD) simul...

The MM-GBSA binding free energies (kcal/mol) of three different VDR and CYP24A1 models.

Selvaraman Nagamani (819665)
Karthikeyan Muthusamy (819667)

October 2018

The MM-GBSA binding free energies (kcal/mol) of three different VDR and CYP24A1 models.</p

Binding free energy predicted using MM/PBSA calculation for 18, 21 and panduratin A.

Maywan Hariono (6260969)
Sy Bing Choi (4408978)
Ros Fatihah Roslim (6260972)
Mohamed Sufian Nawi (6260975)
Mei Lan Tan (678491)
Ezatul Ezleen Kamarulzaman (6260978)
Nornisah Mohamed (1375221)
Rohana Yusof (401395)
Shatrah Othman (6260981)
Noorsaadah Abd Rahman (550281)
Rozana Othman (677989)
Habibah A. Wahab (1425556)

January 2019

Binding free energy predicted using MM/PBSA calculation for 18, 21 and panduratin A.</p

Binding free energies calculations for peptide-MHC complexes.

Amit Kumar (81180)
Eleonora Cocco (314181)
Luigi Atzori (394676)
Maria Giovanna Marrosu (314216)
Enrico Pieroni (326611)

March 2013

Predisposing (*15:01) and protective (*16:01) alleles bound to MBP and EBNA-1. In column 2 is rep...

Study of the Affinity between the Protein Kinase PKA and Peptide Substrates Derived from Kemptide Using Molecular Dynamics Simulations and MM/GBSA

Mena-Ulecia, K.
Vergara-Jaque, A.
Poblete, H.
Tiznado, W.
Caballero, J.

October 2014

Vergara-Jaque, A (Vergara-Jaque, Ariela); Poblete, H (Poblete, Horacio); Caballero, J (Caballero, Ju...

Hydrogen-Bond occupancies analysis from the results of MD simulations for the peptide-PKA interactions for shorter chain peptides derived from Kemptide (WT).

Karel Mena-Ulecia (596272)
Ariela Vergara-Jaque (638616)
Horacio Poblete (638617)
William Tiznado (596273)
Julio Caballero (531146)

October 2014

a Peptide-PKA heavy atoms that form a HB (Notations of atoms refer to the name of atoms from the ...

Contribution of the interactions energy in kcal/mol of the PspA binding residues in the 3 Å from peptides.

Hassan Mahmood Jindal (750256)
Cheng Foh Le (750257)
Mohd Yasim Mohd Yusof (220988)
Rukumani Devi Velayuthan (750258)
Vannajan Sanghiran Lee (750259)
Sharifuddin Md Zain (750260)
Diyana Mohd Isa (750261)
Shamala Devi Sekaran (165904)

June 2015

Contribution of the interactions energy in kcal/mol of the PspA binding residues in the 3 Å from ...

Total binding free energies of WT-EGFR and EGFRL858R in complex to MIG6-YY, Peptides 5, 6, 10, 26 and 27 obtained by MM-PBSA method.

Farial Tavakoli (6725735)
Mohamad Reza Ganjalikhany (153022)

May 2019

Total binding free energies of WT-EGFR and EGFRL858R in complex to MIG6-YY, Peptides 5, 6, 10, 26 an...

Computing free energies of protein-ligand association

Donnini, S. (Serena)

October 2007

Abstract Spontaneous changes in protein systems, such as the binding of a ligand to an enzyme or rec...

Binding Free-Energy Calculation Is a Powerful Tool for Drug Optimization: Calculation and Measurement of Binding Free Energy for 7‑Azaindole Derivatives to Glycogen Synthase Kinase-3β

Kunihiro Kitamura (1681630)
Yunoshin Tamura (1788742)
Tomokazu Ueki (1788739)
Koji Ogata (494313)
Shigeho Noda (1788745)
Ryutaro Himeno (77159)
Hiroshi Chuman (1788748)

June 2014

Present computational lead (drug)-optimization is lacking in thermodynamic tactics. To examine wheth...

FSH/FSHR binding free energies as computed from GBSA molecular dynamics studies.

Biswa Ranjan Meher (473112)
Anshuman Dixit (163621)
George R. Bousfield (799711)
Gerald H. Lushington (799712)

September 2015

Values are in kcal/mol. Parenthetical values represent standard deviations in the free energies.<...

Predicted relative MM-GBSA free energies (kcal/mol) and individual energy terms of the complexes between shorter chain peptides derived from Kemptide and PKA.

Abstract

Extracted data

Predicted relative MM-GBSA free energies (kcal/mol) and individual energy terms of the complexes between shorter chain peptides derived from Kemptide and PKA.

Abstract

Extracted data

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