Proteins: Structure, Function and Bioinformatics

Journal: Proteins: Structure, Function and Bioinformatics

Abbreviation

Proteins

Publisher

Wiley

ISSN

0887-3585
1097-0134

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Publications 1 - 6 of 6

Ensemble models of proteins and protein domains based on distance distribution restraints
Jeschke, Gunnar (2016)
Proteins: Structure, Function and Bioinformatics
Target highlights in CASP13: Experimental target structures through the eyes of their authors
Lepore, Rosalba; Kryshtafovych, Andriy; Alahuhta, Markus; et al. (2019)
Proteins: Structure, Function and Bioinformatics
Assessment of chemical-crosslink-assisted protein structure modeling in CASP13
Fajardo, J. Eduardo; Shrestha, Rojan; Gil, Nelson; et al. (2019)
Proteins: Structure, Function and Bioinformatics
Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
Lensink, Marc F.; Karasikov, Mikhail; et al. (2019)
Proteins: Structure, Function and Bioinformatics
Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri
Xu, Kehan; Dedic, Emil; Brodersen, Ditlev E. (2016)
Proteins: Structure, Function and Bioinformatics
On the use of intra-molecular distance and angle constraints to lengthen the time step in molecular and stochastic dynamics simulations of proteins
Pechlaner, Maria; van Gunsteren, Wilfred F. (2022)
Proteins: Structure, Function and Bioinformatics
Computer simulation of proteins in aqueous solution at the atomic level of resolution is still limited in time span and system size due to limited computing power available and thus employs a variety of time-saving techniques that trade some accuracy against computational effort. An example of such a time-saving technique is the application of constraints to particular degrees of freedom when integrating Newton's or Langevin's equations of motion in molecular dynamics (MD) or stochastic dynamics (SD) simulations, respectively. The application of bond-length constraints is standard practice in protein simulations and allows for a lengthening of the time step by a factor of three. Applying recently proposed algorithms to constrain bond angles or dihedral angles, it is investigated, using the protein trypsin inhibitor as test molecule, whether bond angles and dihedral angles involving hydrogen atoms or even stiff proper (torsional) dihedral angles as well as improper ones (maintaining particular tetrahedral or planar geometries) may be constrained without generating too many artificial side effects. Constraining the relative positions of the hydrogen atoms in the protein allows for a lengthening of the time step by a factor of two. Additionally constraining the improper dihedral angles and the stiff proper (torsional) dihedral angles in the protein does not allow for an increase of the MD or SD time step.

Publications 1 - 6 of 6

Journal: Proteins: Structure, Function and Bioinformatics

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