Results 41 to 50 of about 7,568,994 (301)
Molecular dynamics simulation in virus research [PDF]
Frontiers in Microbiology, 2012 Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the ...
Hirotaka eOde +8 more
openaire +3 more sources
Modelling stem cell differentiation related processes—A practical overview for biologists
FEBS Letters, EarlyView.Stem cell differentiation is complex and difficult to control experimentally. This review introduces suitable computational modelling approaches that can support stem cell research, from mechanistic ODE and abstract models to multiscale and deep learning methods.
Ricco Zeegelaar +4 more
wiley +1 more source
The structural integrity of human TFF1 under reducing conditions
Redox BiologyThe trefoil factor family (TFF) comprises three secretory peptides (TFF1, TFF2, TFF3) that regulate diverse physiological processes to maintain gastrointestinal mucosal integrity and homeostasis.
Dilsah Nur Elmaci +4 more
doaj +1 more source
Reconstructing enzyme evolution by protein engineering
FEBS Letters, EarlyView.Natural enzyme evolution can be retraced by protein engineering methods such as directed evolution, rational design, and ancestral sequence reconstruction. These approaches reveal how enzymes emerged from ligand‐binding scaffolds, developed varying substrate preferences, formed oligomeric complexes, adapted to environmental changes, and evolved novel ...
Lukas Drexler +2 more
wiley +1 more source
Molecular dynamics simulations of complex systems including HIV-1 protease [PDF]
, 2010 Advances in supercomputer architectures have resulted in a situation where many scienti fic codes are used on systems whose performance characteristics di ffer considerably from the platform they were developed and optimised for.
Kenway, O.A., Kenway, OA
core
Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures [PDF]
, 2013 Coarse grain (CG) molecular models have been proposed to simulate complex sys- tems with lower computational overheads and longer timescales with respect to atom- istic level models.
Acquaviva*, Andrea +11 more
core +1 more source
Computational Spectroscopy and Reaction Dynamics
CHIMIA, 2011 Physico- and bio-chemical processes on the femto- to picosecond time scale are ideally suited to be investigated with all-atom simulations.
Pierre-Andre Cazade +3 more
doaj +1 more source
Electrostatic screening in molecular dynamics simulations [PDF]
"Protein Engineering, Design and Selection", 1991 The screened Coulombic potential has been shown to describe satisfactorily equilibrium properties like pK shifts, the effects of charged groups on redox potentials and binding constants of metal ions. To test how well the screening of the electrostatic potential describes the dynamical trajectory of a macromolecular system, a series of comparative ...
Solmajer T, Mehler EL
openaire +3 more sources
Conserved binding mode but diverse interfaces of MreC‐PBP2 interactions
FEBS Letters, EarlyView.The crystal structure of abMreC reveals a conserved two β‐barrel architecture and provides structural insights into its role within the bacterial elongasome. The abMreC–abPBP2 complex model identifies the molecular basis of MreC‐mediated PBP2 recognition, contributing to the regulation of peptidoglycan synthesis.
Hyunseok Jang +4 more
wiley +1 more source
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch [PDF]
, 2009 Riboswitches are a novel class of genetic control elements that function through the direct interaction of small metabolite molecules with structured RNA elements.
Stock, Gerhard +4 more
core +1 more source