The “Dead-End Elimination” Theorem: A New Approach to the Side-Chain Packing Problem

1994 ◽  
pp. 307-337 ◽  
Author(s):  
Johan Desmet ◽  
Marc De Maeyer ◽  
Ignace Lasters
Keyword(s):  
Packing Problem ◽  
Side Chain ◽  
Chain Packing ◽  
New Approach ◽  
Dead End ◽  
The Dead ◽  
Side Chain Packing

scholarly journals Protein side-chain packing problem: is there still room for improvement?

2016 ◽  
pp. bbw079 ◽  
Author(s):  
José Colbes ◽  
Rosario I. Corona ◽  
Christian Lezcano ◽  
David Rodríguez ◽  
Carlos A. Brizuela
Keyword(s):  
Packing Problem ◽  
Side Chain ◽  
Chain Packing ◽  
Side Chain Packing

PROTEIN SIDE-CHAIN PACKING PROBLEM: A MAXIMUM EDGE-WEIGHT CLIQUE ALGORITHMIC APPROACH

2005 ◽  
Vol 03 (01) ◽  
pp. 103-126 ◽  
Author(s):  
K. C. DUKKA BAHADUR ◽  
ETSUJI TOMITA ◽  
JUN'ICHI SUZUKI ◽  
TATSUYA AKUTSU
Keyword(s):  
Protein Design ◽  
Optimal Solution ◽  
Maximum Clique ◽  
Packing Problem ◽  
Protein Docking ◽  
Side Chain ◽  
Edge Weight ◽  
Chain Packing ◽  
Chain Conformations ◽  
Side Chain Packing

"Protein Side-chain Packing" has an ever-increasing application in the field of bio-informatics, dating from the early methods of homology modeling to protein design and to the protein docking. However, this problem is computationally known to be NP-hard. In this regard, we have developed a novel approach to solve this problem using the notion of a maximum edge-weight clique. Our approach is based on efficient reduction of protein side-chain packing problem to a graph and then solving the reduced graph to find the maximum clique by applying an efficient clique finding algorithm developed by our co-authors. Since our approach is based on deterministic algorithms in contrast to the various existing algorithms based on heuristic approaches, our algorithm guarantees of finding an optimal solution. We have tested this approach to predict the side-chain conformations of a set of proteins and have compared the results with other existing methods. We have found that our results are favorably comparable or better than the results produced by the existing methods. As our test set contains a protein of 494 residues, we have obtained considerable improvement in terms of size of the proteins and in terms of the efficiency and the accuracy of prediction.

Side chain packing states of chitosan‐based supramolecular derivatives containing long alkyl side chains

2020 ◽  
Vol 3 (2) ◽  
Author(s):  
Lingzhi Liu ◽  
Dong Lyu ◽  
Mingyue Xiang ◽  
Yongfeng Men
Keyword(s):  
Side Chain ◽  
Side Chains ◽  
Chain Packing ◽  
Alkyl Side Chains ◽  
Side Chain Packing

scholarly journals Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics

2018 ◽  
Vol 14 (12) ◽  
pp. e1006342 ◽  
Author(s):  
John M. Jumper ◽  
Nabil F. Faruk ◽  
Karl F. Freed ◽  
Tobin R. Sosnick
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Side Chain ◽  
Accurate Calculation ◽  
Chain Packing ◽  
Protein Molecular Dynamics ◽  
Side Chain Packing

scholarly journals The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins

1995 ◽  
Vol 4 (11) ◽  
pp. 2300-2309 ◽  
Author(s):  
Su Yun Chung ◽  
S. Subbiah
Keyword(s):  
Side Chain ◽  
Chain Packing ◽  
Side Chain Packing

Side Chain Packing of the N- and C-Terminal Helices Plays a Critical Role in the Kinetics of CytochromecFolding†

Biochemistry ◽  
1996 ◽  
Vol 35 (17) ◽  
pp. 5538-5549 ◽  
Author(s):  
Wilfredo Colón ◽  
Gülnur A. Elöve ◽  
L. Paul Wakem ◽  
Fred Sherman ◽  
Heinrich Roder
Keyword(s):  
Critical Role ◽  
Side Chain ◽  
Chain Packing ◽  
Kinetics Of ◽  
Side Chain Packing
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