SDA 7: A modular and parallel implementation of the simulation of diffusional association software (Q38498104)

3 September 2017

SDA 7: A modular and parallel implementation of the simulation of diffusional association software (English)

1 reference

3 September 2017

Neil J Bruce

2

0 references

Julia Romanowska

object named as

Julia Romanowska

3

0 references

Rebecca C Wade

object named as

Rebecca C Wade

9

0 references

author name string

Michael Martinez

1

1 reference

3 September 2017

Daria B Kokh

4

1 reference

3 September 2017

Musa Ozboyaci

5

1 reference

3 September 2017

Xiaofeng Yu

6

1 reference

3 September 2017

Mehmet Ali Öztürk

7

1 reference

3 September 2017

Stefan Richter

8

1 reference

3 September 2017

29 June 2015

1 reference

Journal of Computational Chemistry

3 September 2017

1 reference

3 September 2017

36

1 reference

3 September 2017

21

1 reference

3 September 2017

1631-1645

1 reference

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

3 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Biomolecular electrostatics and solvation: a computational perspective

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Browndye: A Software Package for Brownian Dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Generalized Born model with a simple, robust molecular volume correction

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Comparison of multiple Amber force fields and development of improved protein backbone parameters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Electrostatics of nanosystems: application to microtubules and the ribosome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Aqueous Solvent

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Characterization of the Ligand Receptor Encounter Complex and Its Potential for in Silico Kinetics-Based Drug Development

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Atomistic simulations of competition between substrates binding to an enzyme

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Brownian dynamics simulation of protein solutions: structural and dynamical properties

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Brownian dynamics simulation of protein-protein diffusional encounter

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Finding a needle in a haystack: the role of electrostatics in target lipid recognition by PH domains.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

On the structure and dynamics of the complex of the nucleosome and the linker histone

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Simulation of the diffusional association of barnase and barstar.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Hydrodynamics of macromolecular complexes. III. Bacterial viruses.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

The impact of viral RNA on the association rates of capsid protein assembly: bacteriophage MS2 as a case study

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Protein-protein docking by simulating the process of association subject to biochemical constraints.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4755232

Equation of State Calculations by Fast Computing Machines

31 August 2018

1 reference

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

21 January 2018

1 reference

On the Contributions of Diffusion and Thermal Activation to Electron Transfer betweenPhormidium laminosumPlastocyanin and Cytochromef: Brownian Dynamics Simulations with Explicit Modeling of Nonpolar Desolvation Interactions and Electron Transfer Eve

21 January 2018

1 reference

Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations

21 January 2018

1 reference

GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26123630

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Rapid, electrostatically assisted association of proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26123630

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/JCC.23971

1 reference

journals/jcc/MartinezBRKOYO015

3 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

3 September 2017

PubMed publication ID

26123630

1 reference