ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB

JA Maier, C Martinez, K Kasavajhala… - Journal of chemical …, 2015 - ACS Publications
… We were unable to exhaustively explore side chain conformational space side chains with
more than two rotatable bonds. Tyrosine has three rotatable χ bonds, but dihedral space is …

[HTML][HTML] The interrelationships of side-chain and main-chain conformations in proteins

P Chakrabarti, D Pal - Progress in biophysics and molecular biology, 2001 - Elsevier
… Å) and flipping of the planar side chains (when required by atomic … side chain on the
main-chain conformation by analysing the interrelationship between the side-chain and main-chain

Side chain engineering in solution-processable conjugated polymers

J Mei, Z Bao - Chemistry of Materials, 2014 - ACS Publications
… Some recent studies have begun to focus on side chain engineering, collectively observing
side chains used in conjugated polymers. Next, some recent examples in which side chain

Extending the accuracy limits of prediction for side-chain conformations

Z Xiang, B Honig - Journal of molecular biology, 2001 - Elsevier
side-chain, exploring all possible combinations of side-chain … sufficient to yield accurate
predictions for buried side-chains. … in the prediction of side-chain conformations. The Ponder & …

Synthesis of side-chain modified polypeptides

TJ Deming - Chemical reviews, 2016 - ACS Publications
Proteins have long fascinated scientists since their complex sequences and diversity of chemical
functionality can lead to structurally defined folded chains with highly specific biological …

Sidechain flexibility in proteins upon ligand binding

R Najmanovich, J Kuttner, V Sobolev… - Proteins: Structure …, 2000 - Wiley Online Library
… of amino-acid side chains belonging to binding pocket residues need to be considered
flexible at any one time in a search algorithm (eg, amino-acid side chains of three or fewer …

Evidence of a novel side chain structure in regioregular poly (3-alkylthiophenes)

TJ Prosa, MJ Winokur, RD McCullough - Macromolecules, 1996 - ACS Publications
… of the side chains. Structure factor intensity calculations 9 support a model in which these
side chains are strongly tilted at an angle such that this side chain nesting approximates a 4.5 …

Backbone-dependent rotamer library for proteins application to side-chain prediction

RL Dunbrack Jr, M Karplus - Journal of molecular biology, 1993 - Elsevier
… Introduction An understanding of the conformations of sidechains is required for the … by
providing a procedure for the initial placement of side-chains. They form part of any scheme to …

Improved prediction of protein sidechain conformations with SCWRL4

GG Krivov, MV Shapovalov… - … Structure, Function, and …, 2009 - Wiley Online Library
… Determination of side-chain conformations is an important … density of the side chains
demonstrate that side chains with higher … Among side chains with higher electron density (25–100th …

On the role of the crystal environment in determining protein side-chain conformations

MP Jacobson, RA Friesner, Z Xiang, B Honig - Journal of molecular biology, 2002 - Elsevier
side-chain conformations. Our results are also relevant to the understanding of changes in
side-chain … how side-chain conformations change in response to their local environment. …