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There are 43304 results for: content related to: Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling

  1. Flexible docking and refinement with a coarse-grained protein model using ATTRACT

    Proteins: Structure, Function, and Bioinformatics

    Volume 81, Issue 12, December 2013, Pages: 2167–2174, Sjoerd de Vries and Martin Zacharias

    Version of Record online : 17 OCT 2013, DOI: 10.1002/prot.24400

  2. Modeling Complexes of Transmembrane Proteins: Systematic Analysis of Protein[BOND]Protein Docking Tools

    Molecular Informatics

    Volume 32, Issue 8, August 2013, Pages: 717–733, Agnieszka A. Kaczor, Jana Selent, Ferran Sanz and Manuel Pastor

    Version of Record online : 6 AUG 2013, DOI: 10.1002/minf.201200150

  3. Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 9, August 2012, Pages: 2207–2217, Raed Khashan, Weifan Zheng and Alexander Tropsha

    Version of Record online : 7 JUN 2012, DOI: 10.1002/prot.24110

  4. Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model

    Proteins: Structure, Function, and Bioinformatics

    Volume 51, Issue 1, 1 April 2003, Pages: 21–40, Paul I. W. de Bakker, Mark A. DePristo, David F. Burke and Tom L. Blundell

    Version of Record online : 8 FEB 2003, DOI: 10.1002/prot.10235

  5. EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization

    Proteins: Structure, Function, and Bioinformatics

    Volume 67, Issue 4, June 2007, Pages: 1010–1025, Aurélien Grosdidier, Vincent Zoete and Olivier Michielin

    Version of Record online : 22 MAR 2007, DOI: 10.1002/prot.21367

  6. Scoring optimisation of unbound protein–protein docking including protein binding site predictions

    Journal of Molecular Recognition

    Volume 25, Issue 1, January 2012, Pages: 15–23, Sebastian Schneider and Martin Zacharias

    Version of Record online : 12 DEC 2011, DOI: 10.1002/jmr.1165

  7. Structure determination of a protein assembly by amino acid selective cross-saturation

    Proteins: Structure, Function, and Bioinformatics

    Volume 79, Issue 1, January 2011, Pages: 179–190, Eiji Kanamori, Shunsuke Igarashi, Masanori Osawa, Yoshifumi Fukunishi, Ichio Shimada and Haruki Nakamura

    Version of Record online : 15 OCT 2010, DOI: 10.1002/prot.22871

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    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

  9. Clustering biomolecular complexes by residue contacts similarity

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 7, July 2012, Pages: 1810–1817, João P. G. L. M. Rodrigues, Mikaël Trellet, Christophe Schmitz, Panagiotis Kastritis, Ezgi Karaca, Adrien S. J. Melquiond and Alexandre M. J. J. Bonvin

    Version of Record online : 8 MAY 2012, DOI: 10.1002/prot.24078

  10. Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein–protein docking

    Proteins: Structure, Function, and Bioinformatics

    Volume 70, Issue 3, 15 February 2008, Pages: 794–809, Andreas May and Martin Zacharias

    Version of Record online : 29 AUG 2007, DOI: 10.1002/prot.21579

  11. The size of the intermolecular energy funnel in protein–protein interactions

    Proteins: Structure, Function, and Bioinformatics

    Volume 72, Issue 1, July 2008, Pages: 344–352, Jagtar Hunjan, Andrey Tovchigrechko, Ying Gao and Ilya A. Vakser

    Version of Record online : 23 JAN 2008, DOI: 10.1002/prot.21930

  12. Intuitive, but not simple: Including explicit water molecules in protein–protein docking simulations improves model quality

    Proteins: Structure, Function, and Bioinformatics

    Volume 82, Issue 6, June 2014, Pages: 916–932, Hardik I. Parikh and Glen E. Kellogg

    Version of Record online : 9 DEC 2013, DOI: 10.1002/prot.24466

  13. Feature-based classification of native and non-native protein–protein interactions: Comparing supervised and semi-supervised learning approaches

    PROTEOMICS

    Volume 11, Issue 22, No. 22 November 2011, Pages: 4321–4330, Nan Zhao, Bin Pang, Chi-Ren Shyu and Dmitry Korkin

    Version of Record online : 17 OCT 2011, DOI: 10.1002/pmic.201100217

  14. RNA approaches the B-form in stacked single strand dinucleotide contexts

    Biopolymers

    Volume 105, Issue 2, February 2016, Pages: 65–82, Ada Sedova and Nilesh K. Banavali

    Version of Record online : 24 NOV 2015, DOI: 10.1002/bip.22750

  15. Binding site prediction and improved scoring during flexible protein–protein docking with ATTRACT

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 15, 15 November 2010, Pages: 3131–3139, Sébastien Fiorucci and Martin Zacharias

    Version of Record online : 29 JUN 2010, DOI: 10.1002/prot.22808

  16. Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: Application in the refinement of de novo models

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 7, July 2012, Pages: 1744–1754, Hao Fan, Xavier Periole and Alan E. Mark

    Version of Record online : 13 APR 2012, DOI: 10.1002/prot.24068

  17. pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein–protein docking

    Proteins: Structure, Function, and Bioinformatics

    Volume 68, Issue 2, 1 August 2007, Pages: 503–515, Tammy Man-Kuang Cheng, Tom L. Blundell and Juan Fernandez-Recio

    Version of Record online : 19 APR 2007, DOI: 10.1002/prot.21419

  18. iATTRACT: Simultaneous global and local interface optimization for protein–protein docking refinement

    Proteins: Structure, Function, and Bioinformatics

    Volume 83, Issue 2, February 2015, Pages: 248–258, Christina E. M. Schindler, Sjoerd J. de Vries and Martin Zacharias

    Version of Record online : 18 DEC 2014, DOI: 10.1002/prot.24728

  19. High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations

    Proteins: Structure, Function, and Bioinformatics

    Volume 82, Issue 8, August 2014, Pages: 1624–1635, Hiroki Shirai, Kazuyoshi Ikeda, Kazuo Yamashita, Yuko Tsuchiya, Jamica Sarmiento, Shide Liang, Tatsuaki Morokata, Kenji Mizuguchi, Junichi Higo, Daron M. Standley and Haruki Nakamura

    Version of Record online : 13 MAY 2014, DOI: 10.1002/prot.24591

  20. A combination of rescoring and refinement significantly improves protein docking performance

    Proteins: Structure, Function, and Bioinformatics

    Volume 72, Issue 1, July 2008, Pages: 270–279, Brian Pierce and Zhiping Weng

    Version of Record online : 23 JAN 2008, DOI: 10.1002/prot.21920