Results 11 to 20 of about 7,119,113 (404)

Side-Chain and Backbone Ordering in Homopolymers [PDF]

The Journal of Physical Chemistry B, 2007
In order to study the relation between backbone and side chain ordering in proteins, we have performed multicanonical simulations of deka-peptide chains with various side groups. Glu10, Gln10, Asp10, Asn10, and Lys10 were selected to cover a wide variety of possible interactions between the side chains of the monomers.
Yanjie Wei, Walter Nadler, Ulrich H. E. Hansmann   +2 more
openaire   +5 more sources

Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models [PDF]

, 2004
In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We distinguish effects due to chirality and effects due to side chain flexibilities, since residues in proteins are L ...
Bagci, Black, Brady, Bromberg, Chan, Cole, Creamer, Creamer, Cronin, Dill, Dima, Doig, Dukor, Dunbrack, Dunbrack, Dunbrack, Hill, Jie Liang, Jinfeng Zhang, Kirshenbaum, Klimov, Kussell, Kussell, Lau, Liang, Liang, Liu, Lovell, Micheletti, Miranker, Mitchell, Park, Pickett, Richards, Richards, Rong Chen, Schafer, Shakhnovich, Tekaia, Wynn, Xia, Yu, Yu Chen, Zhang   +43 more
arxiv   +3 more sources

An Exact Algorithm for Side-Chain Placement in Protein Design [PDF]

, 2011
Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial side-chain placement problem consists of choosing a side-chain placement for each residue position such that the resulting
A. Hildebrandt, A.A. Canutescu, A.R. Leach, B. Chazelle, B. Kuhlman, C. Voigt, C. Yanover, C.L. Kingsford, D. Sontag, E. Althaus, G. Dantas, G. Dantas, Gunnar W. Klau, J. Desmet, J. Desmet, J. Xu, J.D. Bloom, K. Mehlhorn, L. Wernisch, M. Held, N.A. Pierce, N.A. Pierce, Nora C. Toussaint, P.S. Shah, R.F. Goldstein, R.L. Dunbrack, Stefan Canzar, W. Xie, Z. Xiang   +28 more
arxiv   +10 more sources

Monte Carlo simulations reveal the straightening up of an end-grafted flexible chain with a rigid side chain [PDF]

, 2007
We have studied the conformational properties of a flexible end-grafted chain (length $N$) with a rigid side chain (length $S$) by means of Monte Carlo simulations. Depending on the lengths $N$ and $S$ and the branching site, $b$, we observe a considerable straightening of the flexible backbone as quantified via the gyration tensor.
A. Halperin, Dieter W. Heermann, K. Binder, Marcel Hellmann, Matthias Weiss   +4 more
arxiv   +3 more sources

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

Journal of Chemical Theory and Computation, 2015
Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in
James Maier, Carmenza Martinez, Koushik Kasavajhala, L. Wickstrom, Kevin Hauser, Carlos Simmerling   +5 more
semanticscholar   +1 more source

Cephalosporins: A Focus on Side Chains and β-Lactam Cross-Reactivity

Pharmacy, 2019
Cephalosporins are among the most commonly prescribed antibiotic classes due to their wide clinical utility and general tolerability, with approximately 1−3% of the population reporting a cephalosporin allergy. However, clinicians may avoid the use
Saira B. Chaudhry, Michael P. Veve, Jamie L. Wagner   +2 more
doaj   +1 more source

Evolutionary couplings detect side-chain interactions [PDF]

PeerJ, 2019
Patterns of amino acid covariation in large protein sequence alignments can inform the prediction of de novo protein structures, binding interfaces, and mutational effects.
Adam J. Hockenberry, Claus O. Wilke
doaj   +2 more sources

Improved side-chain torsion potentials for the Amber ff99SB protein force field

Proteins: Structure, Function, and Bioinformatics, 2010
Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these ...
K. Lindorff-Larsen, S. Piana, Kim Palmo, P. Maragakis, J. L. Klepeis, R. Dror, D. Shaw   +6 more
semanticscholar   +1 more source

Design and Investigation of a Side-Chain Liquid Crystalline Polysiloxane with a N_tb-Phase-Forming Side Chain

Crystals, 2023
A new mesogenic non-symmetric dimeric monomer with a terminal olefin function, forming a twist bend nematic (Ntb) as well as a nematic (N) phase, was synthesized, using an enhanced synthetic methodology, which avoids isomerization of the terminal double ...
Wanhe Jiang, Georg H. Mehl
doaj   +1 more source

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

Journal of Chemical Theory and Computation, 2012
While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large number of applications, limitations in the model with respect to the equilibrium between the sampling of helical and extended conformations ...
R. Best, Xiao Zhu, Jihyun Shim, Pedro E. M. Lopes, J. Mittal, M. Feig, Alexander D. MacKerell   +6 more
semanticscholar   +1 more source