Results 21 to 30 of about 7,932,784 (254)

Molecular Dynamics Simulations of Deformable Viral Capsomers

Viruses, 2023
Most coarse-grained models of individual capsomers associated with viruses employ rigid building blocks that do not exhibit shape adaptation during self-assembly.
Lauren B. Nilsson, Fanbo Sun, J. C. S. Kadupitiya, Vikram Jadhao   +3 more
doaj   +1 more source

Quality assurance for biomolecular simulations [PDF]

, 2006
Contemporary structural biology has an increased emphasis on high- throughput methods. Biomolecular simulations can add value to structural biology via the provision of dynamic information. However, at present there are no agreed measures for the quality
Wu, Bing, Ng, Muan Hong, Tai, Kaihsu, Johnston, Steven, Fangohr, Hans, Essex, Jonathan W, Sansom, Mark S. P., Sansom, Mark S.P., Murdock, Stuart E., Laughton, Charles A.   +9 more
core   +1 more source

Molecular dynamics simulations reveal that AEDANS is an inert fluorescent probe for the study of membrane proteins [PDF]

, 2009
Computer simulations were carried out of a number of AEDANS-labeled single cysteine mutants of a small reference membrane protein, M13 major coat protein, covering 60% of its primary sequence.
Hemminga, M.A., Schor, M., D. Peter Tieleman, Marieke Schor, Tieleman, D.P., Baumgaertner, A., Marcus A. Hemminga, Vos, W.L., Werner L. Vos, Artur Baumgaertner   +9 more
core   +1 more source

Computational Studies on the Inhibitor Selectivity of Human JAMM Deubiquitinylases Rpn11 and CSN5

Frontiers in Chemistry, 2018
Deubiquitinylases (DUBs) are highly specialized enzymes which are responsible for removal of covalently attached ubiquitin(s) from the targeted proteins. DUBs play an important role in maintaining the protein homeodynamics. Recently, DUBs have emerged as
Vikash Kumar, Vikash Kumar, Michael Naumann, Matthias Stein   +3 more
doaj   +1 more source

Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations [PDF]

, 2011
Computer simulation of protein dynamics offers unique high-resolution information that complements experiment. Using experimentally derived structures of the natively folded prion protein (PrP), physically realistic dynamics and conformational changes ...
Valerie Daggett, Daggett, Valerie, van der Kamp, Marc W, Marc W. van der Kamp   +3 more
core   +1 more source

Crossing the Boundaries within Computational Chemistry: From Molecular Dynamics to Cheminformatics and back

CHIMIA, 2014
The research in the group for computational chemistry at the ETH Zurich focuses on the development of methods and software for classical molecular dynamics simulations and cheminformatics, and their application to biological and chemical ...
Sereina Riniker
doaj   +1 more source

Computational Design of Nanobody Binding to Cortisol to Improve Their Binding Affinity Using Molecular Docking and Molecular Dynamics Simulations

Indonesian Journal of Chemistry, 2022
Currently, nanobody binding cortisol has been deposited in the database. Unfortunately, the affinity is still in micromolar order. Substituting hydrophobic residues in the binding pocket and utilizing CDR2 and CDR3 is the strategy to improve the affinity.
Umi Baroroh, Nur Asni Setiani, Irma Mardiah, Dewi Astriany, Muhammad Yusuf   +4 more
doaj   +1 more source

Pulling polymers on energetically disordered surfaces: molecular dynamics tests of linear and non-linear response [PDF]

, 2013
We present equilibrium and non-equilibrium molecular dynamics simulations of flexible polymer chains absorbed on heterogeneous surfaces. The surfaces are flat but energetically disordered, as they consist of a random mixture of weakly and more strongly ...
Sluckin, Tim, Timothy J. Sluckin, Raos, Guido   +2 more
core   +1 more source

Conformational Changes of Glutamine 5′-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations

Frontiers in Chemistry, 2021
Glutamine 5′-phosphoribosylpyrophosphate amidotransferase (GPATase) catalyzes the synthesis of phosphoribosylamine, pyrophosphate, and glutamate from phosphoribosylpyrophosphate, as well as glutamine at two sites (i.e., glutaminase and ...
Congcong Li, Siao Chen, Tianci Huang, Fangning Zhang, Jiawei Yuan, Hao Chang, Wannan Li, Weiwei Han   +7 more
doaj   +1 more source

Molecular dynamics simulations and drug discovery

BMC Biology, 2011
This review discusses the many roles atomistic computer simulations of macromolecular (for example, protein) receptors and their associated small-molecule ligands can play in drug discovery, including the identification of cryptic or allosteric binding ...
Durrant Jacob D, McCammon J Andrew
doaj   +1 more source