Inter-subunit interaction energies during molecular dynamics simulations.

Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes

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Calculating Free Energies Using Scaled-force Molecular Dynamics Algorithm. Molecular Simulation 28

Eric Darve
Michael A. Wilsony
Andrew Pohorilley

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One common objective of molecular simulations in chemistry and biology is to calcu-late the free ene...

Inter-subunit interaction distances during molecular dynamics 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

A) Variation of the atomic distance d(R/H681, CA - H679’, O) as a characteristic proximal inter-s...

Interaction energies measured between Fel d 1 monomers during molecular dynamics simulations under different force fields (kJ/mol).

Rodrigo Ligabue-Braun (471939)
Liana Guimarães Sachett (764394)
Laércio Pol-Fachin (442012)
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Interaction energies measured between Fel d 1 monomers during molecular dynamics simulations unde...

Inter-protein orientations and interaction energies along the simulation trajectories.

Jaya C. Jose (628467)
Prathit Chatterjee (628468)
Neelanjana Sengupta (618674)

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The inter-protein center of mass distances (in Å) at the start of the unbiased simulations is den...

Interaction energy profile with representative snapshots.

Stefan Gahbauer (3331956)
Kristyna Pluhackova (1847899)
Rainer A. Böckmann (330653)

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The energy profile shows the interaction energy (estimated as the sum of Lennard-Jones and Coulom...

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Interactions between coevolving residues in GP120.

Yuqi Zhao (3512822)
Yanjie Wang (444557)
Yuedong Gao (691658)
Gonghua Li (691659)
Jingfei Huang (240104)

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(A) The contact (hydrogen bonds) maps from molecular dynamics simulation of GP120; (B-F) Snapshot...

The application of molecular dynamics simulation techniques and free energy

Pieffet, Gilles

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Proteins are the media through which genetic information is expressed. They are involved in most if ...

Potential energies and number of hydrogen bonds between different components of simulated p19 systems.

Jane R. Allison (105090)
Marcus Lechner (618023)
Marc P. Hoeppner (124332)
Anthony M. Poole (124334)

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Systems comprise wild-type and all permissible mutations of p19 alone or in complex with t...

A link between two-body and three-body interaction energies in fluids

Sadus, Richard J.
Gianluca Marcelli

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Advances in molecular simulation algorithms coupled with rapid growth in the calculation speed of mo...

cit S 1

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the RCSB Protein Data Bank (pdb) † is a simple yet energy arises mainly from a handful of dominant i...

Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes

Almlöf, Martin

January 2007

The ability to accurately predict binding free energies from computer simulations is an invaluable r...

Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes

Almlöf, Martin

January 2007

The ability to accurately predict binding free energies from computer simulations is an invaluable r...

DataSheet1_A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations.PDF

Juliette Martin (45103)
Elisa Frezza (1404622)

October 2022

Protein-protein interactions are at the basis of many protein functions, and the knowledge of 3D str...

Calculating Free Energies Using Scaled-force Molecular Dynamics Algorithm. Molecular Simulation 28

Eric Darve
Michael A. Wilsony
Andrew Pohorilley

January 2002

One common objective of molecular simulations in chemistry and biology is to calcu-late the free ene...

Inter-subunit interaction distances during molecular dynamics 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

A) Variation of the atomic distance d(R/H681, CA - H679’, O) as a characteristic proximal inter-s...

Interaction energies measured between Fel d 1 monomers during molecular dynamics simulations under different force fields (kJ/mol).

Rodrigo Ligabue-Braun (471939)
Liana Guimarães Sachett (764394)
Laércio Pol-Fachin (442012)
Hugo Verli (344202)

July 2015

Interaction energies measured between Fel d 1 monomers during molecular dynamics simulations unde...

Inter-protein orientations and interaction energies along the simulation trajectories.

Jaya C. Jose (628467)
Prathit Chatterjee (628468)
Neelanjana Sengupta (618674)

September 2014

The inter-protein center of mass distances (in Å) at the start of the unbiased simulations is den...

Interaction energy profile with representative snapshots.

Stefan Gahbauer (3331956)
Kristyna Pluhackova (1847899)
Rainer A. Böckmann (330653)

March 2018

The energy profile shows the interaction energy (estimated as the sum of Lennard-Jones and Coulom...

Energetics of π-π Stacking Interactions: Implications in the Phase Separation of Intrinsically Disordered Proteins

Guljas, Andrea

June 2021

π-π stacking interactions are found throughout the proteome and have been shown to play a role in th...

The application of molecular dynamics simulation techniques and free energy

Pieffet, Gilles Paul,

January 2005

Proteins are the media through which genetic information is expressed. They are involved in most if ...

Interactions between coevolving residues in GP120.

Yuqi Zhao (3512822)
Yanjie Wang (444557)
Yuedong Gao (691658)
Gonghua Li (691659)
Jingfei Huang (240104)

February 2015

(A) The contact (hydrogen bonds) maps from molecular dynamics simulation of GP120; (B-F) Snapshot...

The application of molecular dynamics simulation techniques and free energy

Pieffet, Gilles

January 2005

Proteins are the media through which genetic information is expressed. They are involved in most if ...

Potential energies and number of hydrogen bonds between different components of simulated p19 systems.

Jane R. Allison (105090)
Marcus Lechner (618023)
Marc P. Hoeppner (124332)
Anthony M. Poole (124334)

February 2016

Systems comprise wild-type and all permissible mutations of p19 alone or in complex with t...

A link between two-body and three-body interaction energies in fluids

Sadus, Richard J.
Gianluca Marcelli

January 2000

Advances in molecular simulation algorithms coupled with rapid growth in the calculation speed of mo...

cit S 1

Technology Takayama

January 2015

the RCSB Protein Data Bank (pdb) † is a simple yet energy arises mainly from a handful of dominant i...

Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes

Almlöf, Martin

January 2007

The ability to accurately predict binding free energies from computer simulations is an invaluable r...

Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes

Almlöf, Martin

January 2007

The ability to accurately predict binding free energies from computer simulations is an invaluable r...

DataSheet1_A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations.PDF

Juliette Martin (45103)
Elisa Frezza (1404622)

October 2022

Protein-protein interactions are at the basis of many protein functions, and the knowledge of 3D str...

Calculating Free Energies Using Scaled-force Molecular Dynamics Algorithm. Molecular Simulation 28

Eric Darve
Michael A. Wilsony
Andrew Pohorilley

January 2002

One common objective of molecular simulations in chemistry and biology is to calcu-late the free ene...

Inter-subunit interaction energies during molecular dynamics simulations.

Abstract

Extracted data

Inter-subunit interaction energies during molecular dynamics simulations.

Abstract

Extracted data

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