scholarly journals Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking

2018 ◽  
Vol 39 (24) ◽  
pp. 2012-2021 ◽  
Author(s):  
Taras Dauzhenka ◽  
Petras J. Kundrotas ◽  
Ilya A. Vakser
Keyword(s):  
Protein Docking ◽  
Exhaustive Search ◽  
Side Chain ◽  
Chain Conformations

Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations

2003 ◽  
Vol 331 (1) ◽  
pp. 281-299 ◽  
Author(s):  
Jeffrey J. Gray ◽  
Stewart Moughon ◽  
Chu Wang ◽  
Ora Schueler-Furman ◽  
Brian Kuhlman ◽  
...  
Keyword(s):  
Rigid Body ◽  
Protein Docking ◽  
Simultaneous Optimization ◽  
Side Chain ◽  
Rigid Body Displacement ◽  
Chain Conformations

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.

Stereospecific Association of C-20 Epimers of 3β-Hydroxy-16-oxo-24-nor-17-azachol-5-eno-23-nitryle

1997 ◽  
Vol 52 (6) ◽  
pp. 749-756
Author(s):  
Zofia Plesnar ◽  
Stanisław Malanowski ◽  
Zenon Lotowski ◽  
Jacek W. Morzycki ◽  
Jadwiga Frelek ◽  
...  
Keyword(s):  
Proton Nuclear Magnetic Resonance ◽  
Side Chain ◽  
Water Molecules ◽  
Carbonyl Groups ◽  
Nmr Data ◽  
Molecular Modelling Studies ◽  
Modelling Studies ◽  
Lactam Carbonyl ◽  
Self Association ◽  
Chain Conformations

Abstract The cryoscopic measurements show that title compounds are strongly associated in CHCl3 solutions. The association of the 20 R epimer is distinctly less pronounced than that of the 20 S epipmer. Self-association of the 20 S epimer leads to the formation of very large com­plexes. The 20 R epimer forms associates via water molecules. The dissimilarity may be ex­plained in terms of different accessibility of the lactam carbonyl groups in the two epimers for the association. It is proposed that the association process is controlled by the configura­tion at the carbon atom C(20) and conformation around the C(20)-C(22) bond. Populations of side chain conformations of both epimers were determined by means of proton nuclear magnetic resonance. It was found for the 20 R epimer that the t and the -g rotamers are almost equally populated, and the rotamer +g is excluded. For the 20 S epimer the +g rotamer predominates over the t one, and the -g rotamer is excluded. The NMR data are fully consistent with the results of the molecular modelling studies.

scholarly journals Refinement of Protein Docking with Atom-Atom Contact Potentials, Backbone Flexibility and Side-Chain Repacking

2017 ◽  
Vol 112 (3) ◽  
pp. 54a
Author(s):  
Taras Dauzhenka ◽  
Ivan Anishchenko ◽  
Petras J. Kundrotas ◽  
Ilya A. Vakser
Keyword(s):  
Protein Docking ◽  
Side Chain ◽  
Backbone Flexibility

The influence of side-chain conformations on the phase behavior of bottlebrush block polymers

Soft Matter ◽  
2020 ◽  
Vol 16 (34) ◽  
pp. 8047-8056
Author(s):  
Yuguo Chen ◽  
Xinghua Zhang ◽  
Ying Jiang
Keyword(s):  
Self Assembly ◽  
Side Chain ◽  
Chain Model ◽  
Block Polymers ◽  
Consistent Field ◽  
Self Consistent Field ◽  
Self Consistent Field Theory ◽  
Assembly Behavior ◽  
Wormlike Chain Model ◽  
Chain Conformations

A self-consistent field theory based on the wormlike chain model is implemented in the investigation of the self-assembly behavior of bottlebrush block polymers in the formation of a lamellar phase.

Docking and scoring with alternative side-chain conformations

2009 ◽  
Vol 74 (3) ◽  
pp. 712-726 ◽  
Author(s):  
Christoph Hartmann ◽  
Iris Antes ◽  
Thomas Lengauer
Keyword(s):  
Side Chain ◽  
Docking And Scoring ◽  
Chain Conformations

scholarly journals Collective repacking reveals that the structures of protein cores are uniquely specified by steric repulsive interactions

2017 ◽  
Vol 30 (5) ◽  
pp. 387-394 ◽  
Author(s):  
J.C. Gaines ◽  
A. Virrueta ◽  
D.A. Buch ◽  
S.J. Fleishman ◽  
C.S. O'Hern ◽  
...  
Keyword(s):  
Hard Sphere ◽  
Protein Structures ◽  
Standard Test ◽  
Protein Modeling ◽  
Side Chain ◽  
Hard Sphere Model ◽  
Sphere Model ◽  
Modeling Software ◽  
High Prediction ◽  
Chain Conformations

Abstract Protein core repacking is a standard test of protein modeling software. A recent study of six different modeling software packages showed that they are more successful at predicting side chain conformations of core compared to surface residues. All the modeling software tested have multicomponent energy functions, typically including contributions from solvation, electrostatics, hydrogen bonding and Lennard–Jones interactions in addition to statistical terms based on observed protein structures. We investigated to what extent a simplified energy function that includes only stereochemical constraints and repulsive hard-sphere interactions can correctly repack protein cores. For single residue and collective repacking, the hard-sphere model accurately recapitulates the observed side chain conformations for Ile, Leu, Phe, Thr, Trp, Tyr and Val. This result shows that there are no alternative, sterically allowed side chain conformations of core residues. Analysis of the same set of protein cores using the Rosetta software suite revealed that the hard-sphere model and Rosetta perform equally well on Ile, Leu, Phe, Thr and Val; the hard-sphere model performs better on Trp and Tyr and Rosetta performs better on Ser. We conclude that the high prediction accuracy in protein cores obtained by protein modeling software and our simplified hard-sphere approach reflects the high density of protein cores and dominance of steric repulsion.

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