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 …
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 …
main-chain conformation by analysing the interrelationship between the side-chain and main-chain …
Side chain engineering in solution-processable conjugated polymers
… 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 …
… 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 & …
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 …
functionality can lead to structurally defined folded chains with highly specific biological …
Side‐chain 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 …
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 …
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 …
providing a procedure for the initial placement of side-chains. They form part of any scheme to …
Improved prediction of protein side‐chain 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 …
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. …
side-chain … how side-chain conformations change in response to their local environment. …