Interaction energy and interface Accessible Surface Area (ASA) for the VB1OE/huCollp261/HLA-DR4 complexes averaged over the MD simulation runs.

Reassessing buried surface areas in protein-protein complexes.

Chakravarty, Devlina
Guharoy, Mainak
Robert, Charles H.
Chakrabarti, Pinak
Janin, Joel

August 2013

International audienceThe buried surface area (BSA), which measures the size of the interface in a p...

Overall effective interaction energy (Winteq) and the contribution of non-bonded van der Waals (EvdWeq) and Coulomb (ECoueq) interaction energy terms and of the solvation free energy change upon dimerization (ΔGsolveq) averaged over all frames of the equilibrated phase of the productive MD simulations.

Lívia Marton (756117)
Gergely N. Nagy (756118)
Olivér Ozohanics (756119)
Anikó Lábas (756120)
Balázs Krámos (756121)
Julianna Oláh (555121)
Károly Vékey (122026)
Beáta G. Vértessy (24771)

June 2015

The superscript ‘eq’ denotes the equilibrated phase (final 1.75 ns) of the productive MD simulati...

Accessible area calculation of each average structure in MD the simulation.

Nan Wang (21935)
Jiahong Jiang (781283)
Xichen Li (447629)
Hongwei Tan (447628)
Jimin Zheng (447627)
Guangju Chen (104307)
Zongchao Jia (187159)

August 2015

Open/closed apo dimer contains two active pockets and are listed as “first pocket/second pocket” ...

Interaction energy and interface Accessible Surface Area (ASA) in the minimized complexes emerging from docking calculations.

Maria Cristina De Rosa (363356)
Bruno Giardina (75132)
Caterina Bianchi (363357)
Cristiana Carelli Alinovi (363358)
Davide Pirolli (363359)
Gianfranco Ferraccioli (146644)
Maria De Santis (363360)
Gabriele Di Sante (284248)
Francesco Ria (284257)

February 2013

Interaction energy and interface Accessible Surface Area (ASA) in the minimized complexes emergin...

Computational alanine scanning-based free energies for the TCR-VB1OE/huCollp261/HLA-DR4 complex.

Maria Cristina De Rosa (363356)
Bruno Giardina (75132)
Caterina Bianchi (363357)
Cristiana Carelli Alinovi (363358)
Davide Pirolli (363359)
Gianfranco Ferraccioli (146644)
Maria De Santis (363360)
Gabriele Di Sante (284248)
Francesco Ria (284257)

February 2013

Computational alanine scanning-based free energies for the TCR-VB1OE/huCollp261/HLA-DR...

Averaged interaction energy of compound 12 obtained from MD simulation.

Yuno Lee (117275)
Songmi Kim (131671)
Jun Young Kim (511970)
Mahreen Arooj (286338)
Siu Kim (511971)
Swan Hwang (131678)
Byeong-Woo Kim (140529)
Ki Hun Park (511972)
Keun Woo Lee (117280)

January 2014

Averaged interaction energy of compound 12 obtained from MD simulation.</p

Parameters of protein-protein interfaces for the 5′ complex (with pol-β in open conformation and straight DNA).

Alexej Abyzov (44731)
Alper Uzun (44732)
Phyllis R. Strauss (44733)
Valentin A. Ilyin (44734)

February 2013

Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculat...

Parameters of protein-protein interfaces for the 5′ complex (with pol-β in open conformation).

Alexej Abyzov (44731)
Alper Uzun (44732)
Phyllis R. Strauss (44733)
Valentin A. Ilyin (44734)

February 2013

Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculat...

Binding energetics of DGA and CaCCinh-A01 with Ace from MD simulation†.

Tanaya Chatterjee (162479)
Irshad Ali Sheikh (822758)
Devlina Chakravarty (822759)
Pinak Chakrabarti (63526)
Paramita Sarkar (822760)
Tultul Saha (822761)
Manoj K. Chakrabarti (347295)
Kazi Mirajul Hoque (822762)

November 2015

† Interface area and RMSD are calculated after 20 ns of simulationBindin...

Parameters of protein-protein interfaces for the 3′ complex (with pol-β in closed conformation).

Alexej Abyzov (44731)
Alper Uzun (44732)
Phyllis R. Strauss (44733)
Valentin A. Ilyin (44734)

February 2013

Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculat...

Parameters of protein-protein interfaces for the 3′ complex (with pol-β in open conformation).

Alexej Abyzov (44731)
Alper Uzun (44732)
Phyllis R. Strauss (44733)
Valentin A. Ilyin (44734)

February 2013

Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculat...

Calculated structural and energetic quantities for extended MD simulation.

Seyed Hanif Mahboobi (550483)
Alex A. Javanpour (696616)
Mohammad R. K. Mofrad (218868)

February 2015

(A) CRM1-NES-RanGTP—DDX3 interaction energy, (B) RanGTP—DDX3 energy, (C) RMSD, and (D) BSA are pl...

The binding free energy and energy components (kcal/mol) for the four HLA/MICA-TM complexes predicted by the MM/PBSA method.

Sirilak Kongkaew (791375)
Pathumwadee Yotmanee (791376)
Thanyada Rungrotmongkol (791377)
Nopporn Kaiyawet (791378)
Arthitaya Meeprasert (791379)
Toshikatsu Kaburaki (153465)
Hiroshi Noguchi (610885)
Fujio Takeuchi (791380)
Nawee Kungwan (631628)
Supot Hannongbua (791381)

September 2015

HLA alleles area associated orb not associated ...

Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes

Guharoy, Mainak
Chakrabarti, Pinak

January 2009

We report a simple algorithm to scan interfaces in protein-protein complexes for identifying binding...

Estimated parameters characterizing the energy landscape of the MUC1(STn)—MGL interaction.

Soosan Hadjialirezaei (3929486)
Gianfranco Picco (736186)
Richard Beatson (736184)
Joy Burchell (2557957)
Bjørn Torger Stokke (817722)
Marit Sletmoen (736191)

April 2017

Estimated parameters characterizing the energy landscape of the MUC1(STn)—MGL interaction.</p

Reassessing buried surface areas in protein-protein complexes.

Chakravarty, Devlina
Guharoy, Mainak
Robert, Charles H.
Chakrabarti, Pinak
Janin, Joel

August 2013

International audienceThe buried surface area (BSA), which measures the size of the interface in a p...

Overall effective interaction energy (Winteq) and the contribution of non-bonded van der Waals (EvdWeq) and Coulomb (ECoueq) interaction energy terms and of the solvation free energy change upon dimerization (ΔGsolveq) averaged over all frames of the equilibrated phase of the productive MD simulations.

Lívia Marton (756117)
Gergely N. Nagy (756118)
Olivér Ozohanics (756119)
Anikó Lábas (756120)
Balázs Krámos (756121)
Julianna Oláh (555121)
Károly Vékey (122026)
Beáta G. Vértessy (24771)

June 2015

The superscript ‘eq’ denotes the equilibrated phase (final 1.75 ns) of the productive MD simulati...

Accessible area calculation of each average structure in MD the simulation.

Nan Wang (21935)
Jiahong Jiang (781283)
Xichen Li (447629)
Hongwei Tan (447628)
Jimin Zheng (447627)
Guangju Chen (104307)
Zongchao Jia (187159)

August 2015

Open/closed apo dimer contains two active pockets and are listed as “first pocket/second pocket” ...

Interaction energy and interface Accessible Surface Area (ASA) in the minimized complexes emerging from docking calculations.

Maria Cristina De Rosa (363356)
Bruno Giardina (75132)
Caterina Bianchi (363357)
Cristiana Carelli Alinovi (363358)
Davide Pirolli (363359)
Gianfranco Ferraccioli (146644)
Maria De Santis (363360)
Gabriele Di Sante (284248)
Francesco Ria (284257)

February 2013

Interaction energy and interface Accessible Surface Area (ASA) in the minimized complexes emergin...

Computational alanine scanning-based free energies for the TCR-VB1OE/huCollp261/HLA-DR4 complex.

Maria Cristina De Rosa (363356)
Bruno Giardina (75132)
Caterina Bianchi (363357)
Cristiana Carelli Alinovi (363358)
Davide Pirolli (363359)
Gianfranco Ferraccioli (146644)
Maria De Santis (363360)
Gabriele Di Sante (284248)
Francesco Ria (284257)

February 2013

Computational alanine scanning-based free energies for the TCR-VB1OE/huCollp261/HLA-DR...

Averaged interaction energy of compound 12 obtained from MD simulation.

Yuno Lee (117275)
Songmi Kim (131671)
Jun Young Kim (511970)
Mahreen Arooj (286338)
Siu Kim (511971)
Swan Hwang (131678)
Byeong-Woo Kim (140529)
Ki Hun Park (511972)
Keun Woo Lee (117280)

January 2014

Averaged interaction energy of compound 12 obtained from MD simulation.</p

Parameters of protein-protein interfaces for the 5′ complex (with pol-β in open conformation and straight DNA).

Alexej Abyzov (44731)
Alper Uzun (44732)
Phyllis R. Strauss (44733)
Valentin A. Ilyin (44734)

February 2013

Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculat...

Parameters of protein-protein interfaces for the 5′ complex (with pol-β in open conformation).

Alexej Abyzov (44731)
Alper Uzun (44732)
Phyllis R. Strauss (44733)
Valentin A. Ilyin (44734)

February 2013

Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculat...

Binding energetics of DGA and CaCCinh-A01 with Ace from MD simulation†.

Tanaya Chatterjee (162479)
Irshad Ali Sheikh (822758)
Devlina Chakravarty (822759)
Pinak Chakrabarti (63526)
Paramita Sarkar (822760)
Tultul Saha (822761)
Manoj K. Chakrabarti (347295)
Kazi Mirajul Hoque (822762)

November 2015

† Interface area and RMSD are calculated after 20 ns of simulationBindin...

Parameters of protein-protein interfaces for the 3′ complex (with pol-β in closed conformation).

Alexej Abyzov (44731)
Alper Uzun (44732)
Phyllis R. Strauss (44733)
Valentin A. Ilyin (44734)

February 2013

Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculat...

Parameters of protein-protein interfaces for the 3′ complex (with pol-β in open conformation).

Alexej Abyzov (44731)
Alper Uzun (44732)
Phyllis R. Strauss (44733)
Valentin A. Ilyin (44734)

February 2013

Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculat...

Calculated structural and energetic quantities for extended MD simulation.

Seyed Hanif Mahboobi (550483)
Alex A. Javanpour (696616)
Mohammad R. K. Mofrad (218868)

February 2015

(A) CRM1-NES-RanGTP—DDX3 interaction energy, (B) RanGTP—DDX3 energy, (C) RMSD, and (D) BSA are pl...

The binding free energy and energy components (kcal/mol) for the four HLA/MICA-TM complexes predicted by the MM/PBSA method.

Sirilak Kongkaew (791375)
Pathumwadee Yotmanee (791376)
Thanyada Rungrotmongkol (791377)
Nopporn Kaiyawet (791378)
Arthitaya Meeprasert (791379)
Toshikatsu Kaburaki (153465)
Hiroshi Noguchi (610885)
Fujio Takeuchi (791380)
Nawee Kungwan (631628)
Supot Hannongbua (791381)

September 2015

HLA alleles area associated orb not associated ...

Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes

Guharoy, Mainak
Chakrabarti, Pinak

January 2009

We report a simple algorithm to scan interfaces in protein-protein complexes for identifying binding...

Estimated parameters characterizing the energy landscape of the MUC1(STn)—MGL interaction.

Soosan Hadjialirezaei (3929486)
Gianfranco Picco (736186)
Richard Beatson (736184)
Joy Burchell (2557957)
Bjørn Torger Stokke (817722)
Marit Sletmoen (736191)

April 2017

Estimated parameters characterizing the energy landscape of the MUC1(STn)—MGL interaction.</p

Reassessing buried surface areas in protein-protein complexes.

Chakravarty, Devlina
Guharoy, Mainak
Robert, Charles H.
Chakrabarti, Pinak
Janin, Joel

August 2013

International audienceThe buried surface area (BSA), which measures the size of the interface in a p...

Overall effective interaction energy (Winteq) and the contribution of non-bonded van der Waals (EvdWeq) and Coulomb (ECoueq) interaction energy terms and of the solvation free energy change upon dimerization (ΔGsolveq) averaged over all frames of the equilibrated phase of the productive MD simulations.

Lívia Marton (756117)
Gergely N. Nagy (756118)
Olivér Ozohanics (756119)
Anikó Lábas (756120)
Balázs Krámos (756121)
Julianna Oláh (555121)
Károly Vékey (122026)
Beáta G. Vértessy (24771)

June 2015

The superscript ‘eq’ denotes the equilibrated phase (final 1.75 ns) of the productive MD simulati...

Accessible area calculation of each average structure in MD the simulation.

Nan Wang (21935)
Jiahong Jiang (781283)
Xichen Li (447629)
Hongwei Tan (447628)
Jimin Zheng (447627)
Guangju Chen (104307)
Zongchao Jia (187159)

August 2015

Open/closed apo dimer contains two active pockets and are listed as “first pocket/second pocket” ...

Interaction energy and interface Accessible Surface Area (ASA) for the VB1<sup>OE</sup>/huCollp261/HLA-DR4 complexes averaged over the MD simulation runs.

Abstract

Extracted data

Interaction energy and interface Accessible Surface Area (ASA) for the VB1<sup>OE</sup>/huCollp261/HLA-DR4 complexes averaged over the MD simulation runs.

Abstract

Extracted data

Related items

Related items