An improved protein decoy set for testing energy functions for protein structure prediction

Tsai, Jerry, Bonneau, Richard, Morozov, Alexandre V., Kuhlman, Brian, Rohl, Carol A., Baker, David·2003·Proteins: Structure, Function, and Bioinformatics

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  10. A knowledge-based structure-discriminating function that requires only main-chain atom coordinates
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  13. A graph theoretic approach to protein structure selection
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  21. Dynamic and Thermodynamic Signatures of Native and Non-Native Protein States with Application to the Improvement of Protein Structures
    Dawei Li, Rafael Brüschweiler · 2012 · Journal of Chemical Theory and Computation
  22. Assessment of Protein Structure Predictions
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  23. OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling
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  24. Three-Dimensional Ideal Gas Reference State Based Energy Function
    Md Hoque, Avdesh Mishra · 2017 · Current Bioinformatics
  25. Constrained versus unconstrained folding free-energy landscapes
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  26. RNAtive to recognize native-like structure in a set of RNA 3D models
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  27. A novel knowledge-based potential for RNA 3D structure evaluation
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  28. OPUS‐SSF: A side‐chain‐inclusive scoring function for ranking protein structural models
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  29. Divergence, recombination and retention of functionality during protein evolution
    Yanlong O Xu, Randall W. Hall, Richard A. Goldstein, David D. Pollock · 2005 · Human Genomics
  30. Protein Structure Prediction
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  31. OPUS-Refine: A Fast Sampling-Based Framework for Refining Protein Backbone Torsion Angles and Global Conformation
    Gang Xu, Qinghua Wang, Jianpeng Ma · 2020 · Journal of Chemical Theory and Computation
  32. Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction
    Yuangen Yao, Rong Gui, Quan Liu, Ming Yi, Haiyou Deng · 2017 · BMC Bioinformatics
  33. A large decoy set of protein–protein complexes produced by flexible docking
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  34. An Estimate of the Numbers and Density of Low-Energy Structures (or Decoys) in the Conformational Landscape of Proteins
    Kanagasabai Vadivel, N. Gautham · 2009 · PLoS ONE
  35. A Software Pipeline for Protein Structure Prediction
    Michael S. Lee, In‐Chul Yeh, Nela Zavaljevski, Paul Wilson, Jaques Reifman A · 2006
  36. Trajectory-Based Parameterization of a Coarse-Grained Forcefield for High-Thoughput Protein Simulation
    John Jumper, Karl F. Freed, Tobin R. Sosnick · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  37. A Graph Theoretic Approach to Protein Structure Selection
    Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio · 2007 · Lecture notes in computer science
  38. Decoy Database Improvement for Protein Folding
    Hsin-Yi Yeh, Aaron Lindsey, Chih-Peng Wu, Shawna Thomas, Nancy M. Amato · 2015 · Journal of Computational Biology
  39. Template-Based Protein Structure Prediction
    Junfeng Huang, Peng Wei Duan, Wenyan Wu · 2011 · Acta Biophysica Sinica
  40. Improving decoy databases for protein folding algorithms
    Aaron Lindsey, Hsin-Yi Yeh, Chih-Peng Wu, Shawna Thomas, Nancy M. Amato · 2014 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
  41. Coarse‐ and fine‐grained models for proteins: Evaluation by decoy discrimination
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    Richard Bonneau · 2007
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    Yi-Yuan Chiu, Jenn‐Kang Hwang, Jinn‐Moon Yang · 2005 · IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)
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  45. Neural Network Pairwise Interaction Fields for Protein Model Quality Assessment
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  51. Benchmarking the POEM@HOME Network for Protein Structure Prediction
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    Yaohang Li · 2013
  55. Docking HPr to HPr Kinase with Partial Backbone Flexibility By
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  56. Template Based Modeling and Structural Refinement of Protein-Protein Interactions.
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  57. Receptor-free Discrimination of Peptide Native Bound Conformations Suggests Limited Transferability of the “cen_std+score4l” Rosetta Energy Function From Proteins to Peptides
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    Kaizhi Yue · 2022 · Physical review. E