Search Results

There are 10323 results for: content related to: Structure refinement of protein model decoys requires accurate side-chain placement

  1. Detecting local residue environment similarity for recognizing near-native structure models

    Proteins: Structure, Function, and Bioinformatics

    Volume 82, Issue 12, December 2014, Pages: 3255–3272, Hyungrae Kim and Daisuke Kihara

    Version of Record online : 30 OCT 2014, DOI: 10.1002/prot.24658

  2. Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade

    Proteins: Structure, Function, and Bioinformatics

    Jianyi Yang, Wenxuan Zhang, Baoji He, Sara Elizabeth Walker, Hongjiu Zhang, Brandon Govindarajoo, Jouko Virtanen, Zhidong Xue, Hong-Bin Shen and Yang Zhang

    Version of Record online : 18 SEP 2015, DOI: 10.1002/prot.24918

  3. Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models

    Journal of Computational Chemistry

    Volume 34, Issue 20, 30 July 2013, Pages: 1785–1793, Mark A. Olson and Michael S. Lee

    Version of Record online : 23 MAY 2013, DOI: 10.1002/jcc.23325

  4. What is the best reference state for designing statistical atomic potentials in protein structure prediction?

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 9, August 2012, Pages: 2311–2322, Haiyou Deng, Ya Jia, Yanyu Wei and Yang Zhang

    Version of Record online : 18 JUN 2012, DOI: 10.1002/prot.24121

  5. Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction

    Proteins: Structure, Function, and Bioinformatics

    Volume 83, Issue 5, May 2015, Pages: 881–890, Myong-Ho Chae, Florian Krull and Ernst-Walter Knapp

    Version of Record online : 25 MAR 2015, DOI: 10.1002/prot.24782

  6. Tasser-Based Protein Structure Prediction

    Introduction to Protein Structure Prediction: Methods and Algorithms

    Shashi Bhushan Pandit, Hongyi Zhou, Jeffrey Skolnick, Pages: 219–242, 2010

    Published Online : 7 SEP 2010, DOI: 10.1002/9780470882207.ch10

  7. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 7, July 2012, Pages: 1715–1735, Dong Xu and Yang Zhang

    Version of Record online : 13 APR 2012, DOI: 10.1002/prot.24065

  8. REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks

    Proteins: Structure, Function, and Bioinformatics

    Volume 76, Issue 3, 15 August 2009, Pages: 665–676, Yunqi Li and Yang Zhang

    Version of Record online : 23 JAN 2009, DOI: 10.1002/prot.22380

  9. How noise in force fields can affect the structural refinement of protein models?

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 2, February 2012, Pages: 335–341, Pawel Gniewek, Andrzej Kolinski, Robert L Jernigan and Andrzej Kloczkowski

    Version of Record online : 16 DEC 2011, DOI: 10.1002/prot.23240

  10. Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints

    Journal of Computational Chemistry

    Volume 29, Issue 10, 30 July 2008, Pages: 1574–1588, Michal Brylinski and Jeffrey Skolnick

    Version of Record online : 21 FEB 2008, DOI: 10.1002/jcc.20917

  11. You have free access to this content
    On the analysis of protein–protein interactions via knowledge-based potentials for the prediction of protein–protein docking

    Protein Science

    Volume 20, Issue 3, March 2011, Pages: 529–541, Elisenda Feliu, Patrick Aloy and Baldo Oliva

    Version of Record online : 24 FEB 2011, DOI: 10.1002/pro.585

  12. A large decoy set of protein–protein complexes produced by flexible docking

    Journal of Computational Chemistry

    Volume 32, Issue 1, 15 January 2011, Pages: 106–120, Guillaume Launay and Thomas Simonson

    Version of Record online : 17 NOV 2010, DOI: 10.1002/jcc.21604

  13. Extracting knowledge from protein structure geometry

    Proteins: Structure, Function, and Bioinformatics

    Volume 81, Issue 5, May 2013, Pages: 841–851, Peter Røgen and Patrice Koehl

    Version of Record online : 27 FEB 2013, DOI: 10.1002/prot.24242

  14. Durandal: Fast exact clustering of protein decoys

    Journal of Computational Chemistry

    Volume 33, Issue 4, 5 February 2012, Pages: 471–474, Francois Berenger, Rojan Shrestha, Yong Zhou, David Simoncini and Kam Y. J. Zhang

    Version of Record online : 26 NOV 2011, DOI: 10.1002/jcc.21988

  15. Distance-dependent atomic knowledge-based force in protein fold recognition

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 3, March 2012, Pages: 683–690, Mehdi Mirzaie and Mehdi Sadeghi

    Version of Record online : 9 JAN 2012, DOI: 10.1002/prot.24011

  16. Improving threading algorithms for remote homology modeling by combining fragment and template comparisons

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 9, July 2010, Pages: 2041–2048, Hongyi Zhou and Jeffrey Skolnick

    Version of Record online : 18 MAR 2010, DOI: 10.1002/prot.22717

  17. You have free access to this content
    Dental morphology and variation in theropod dinosaurs: Implications for the taxonomic identification of isolated teeth

    The Anatomical Record Part A: Discoveries in Molecular, Cellular, and Evolutionary Biology

    Volume 285A, Issue 2, August 2005, Pages: 699–736, Joshua B. Smith, David R. Vann and Peter Dodson

    Version of Record online : 28 JUN 2005, DOI: 10.1002/ar.a.20206

  18. SVR_CAF: An integrated score function for detecting native protein structures among decoys

    Proteins: Structure, Function, and Bioinformatics

    Volume 82, Issue 4, April 2014, Pages: 556–564, Jianhong Zhou, Wenying Yan, Guang Hu and Bairong Shen

    Version of Record online : 17 OCT 2013, DOI: 10.1002/prot.24421

  19. CyClus: A fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein–protein docking decoys

    Proteins: Structure, Function, and Bioinformatics

    Volume 81, Issue 6, June 2013, Pages: 1005–1016, Satoshi Omori and Akio Kitao

    Version of Record online : 27 FEB 2013, DOI: 10.1002/prot.24252

  20. Template-based protein structure modeling using TASSERVMT

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 2, February 2012, Pages: 352–361, Hongyi Zhou and Jeffrey Skolnick

    Version of Record online : 22 NOV 2011, DOI: 10.1002/prot.23183