Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field

January 2007
BMC Structural Biology;2007, Vol. 7, p43
Academic Journal
No abstract available.


Related Articles

  • High-resolution structure prediction and the crystallographic phase problem. Bin Qian; Raman, Srivatsan; Rhiju Das; Bradley, Philip; McCoy, Airlie J.; Read, Randy J.; Baker, David // Nature;11/8/2007, Vol. 450 Issue 7167, p259 

    The energy-based refinement of low-resolution protein structure models to atomic-level accuracy is a major challenge for computational structural biology. Here we describe a new approach to refining protein structure models that focuses sampling in regions most likely to contain errors while...

  • Protein fragment reconstruction using various modeling techniques. Boniecki, Michal; Rotkiewicz, Piotr; Skolnick, Jeffrey; Kolinski, Andrzej // Journal of Computer-Aided Molecular Design;Nov2003, Vol. 17 Issue 11, p725 

    Recently developed reduced models of proteins with knowledge-based force fields have been applied to a specific case of comparative modeling. From twenty high resolution protein structures of various structural classes, significant fragments of their chains have been removed and treated as...

  • Efficient Sampling in Fragment-Based Protein Structure Prediction Using an Estimation of Distribution Algorithm. Simoncini, David; Zhang, Kam Y. J. // PLoS ONE;Jul2013, Vol. 8 Issue 7, p1 

    Fragment assembly is a powerful method of protein structure prediction that builds protein models from a pool of candidate fragments taken from known structures. Stochastic sampling is subsequently used to refine the models. The structures are first represented as coarse-grained models and then...

  • Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics. Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; KoliƄski, Andrzej // International Journal of Molecular Sciences;May2013, Vol. 14 Issue 5, p9893 

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing...

  • i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10. Bhattacharya, Debswapna; Cheng, Jianlin // PLoS ONE;Jul2013, Vol. 8 Issue 7, p1 

    Protein structure refinement refers to the process of improving the qualities of protein structures during structure modeling processes to bring them closer to their native states. Structure refinement has been drawing increasing attention in the community-wide Critical Assessment of techniques...

  • Interplay of Nkx3.2, Sox9 and Pax3 Regulates Chondrogenic Differentiation of Muscle Progenitor Cells. Cairns, Dana M.; Renjing Liu; Sen, Manpreet; Canner, James P.; Schindeler, Aaron; Little, David G.; Li Zeng // PLoS ONE;Jul2012, Vol. 7 Issue 7, p1 

    Muscle satellite cells make up a stem cell population that is capable of differentiating into myocytes and contributing to muscle regeneration upon injury. In this work we investigate the mechanism by which these muscle progenitor cells adopt an alternative cell fate, the cartilage fate. We show...

  • A Probabilistic Fragment-Based Protein Structure Prediction Algorithm. Simoncini, David; Berenger, Francois; Shrestha, Rojan; Kam Y. J. Zhang // PLoS ONE;Jul2012, Vol. 7 Issue 7, p1 

    Conformational sampling is one of the bottlenecks in fragment-based protein structure prediction approaches. They generally start with a coarse-grained optimization where mainchain atoms and centroids of side chains are considered, followed by a fine-grained optimization with an all-atom...

  • Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations. Allen, Lucy R.; Krivov, Sergei V.; Paci, Emanuele // PLoS Computational Biology;Jul2009, Vol. 5 Issue 7, p1 

    Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio...

  • Prediction of helical peptide folding in an implicit water by a new molecular dynamics scheme with generalized effective potential. Pak, Youngshang; Jang, Soonmin; Shin, Seokmin // Journal of Chemical Physics;4/15/2002, Vol. 116 Issue 15, p6831 

    Previously we demonstrated the effectiveness of the recently developed q-jumping molecular dynamics simulation method (q-jumping MD) in vacuo for fast conformational searches and optimization purposes. In this work we attempt to further investigate the conformational searching capability of this...

  • Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model for Protein Residue-Level Structural Fluctuations. Park, Jun-Koo; Jernigan, Robert; Wu, Zhijun // Bulletin of Mathematical Biology;Jan2013, Vol. 75 Issue 1, p124 

    We investigate several approaches to coarse grained normal mode analysis on protein residual-level structural fluctuations by choosing different ways of representing the residues and the forces among them. Single-atom representations using the backbone atoms C, C, N, and C are considered....


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics