LINUS: a hierarchic procedure to predict the fold of a protein

Cited by (265)

Items 101–200 of 265

1. The development of tertiary interactions during the folding of a large protein
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2. HARMONY: a server for the assessment of protein structures
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3. Ab Initio Protein Folding Using LINUS
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4. Turn scanning by site‐directed mutagenesis: Application to the protein folding problem using the intestinal fatty acid binding protein
   Keehyuk Kim, Carl Frieden · 1998 · Protein Science
5. Protein folding ‐ seeing is deceiving
   George D. Rose · 2021 · Protein Science
6. Three‐dimensional structures and contexts associated with recurrent amino acid sequence patterns
   Karen F. Han, Christopher Bystroff, David A. Baker · 1997 · Protein Science
7. What Determines Protein Folding Type? An Investigation of Intrinsic Structural Properties and its Implications for Understanding Folding Mechanisms
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8. Extraction of interaction potentials between amino acids from native protein structures
   Ruxandra I. Dima, Giovanni Settanni, Cristian Micheletti, Jayanth R. Banavar, Amos Maritan · 2000 · The Journal of Chemical Physics
9. Determination of interaction potentials of amino acids from native protein structures: Tests on simple lattice models
   Jort van Mourik, Cecilia Clementi, Amos Maritan, Flavio Seno, Jayanth R. Banavar · 1999 · The Journal of Chemical Physics
10. Routes are trees: The parsing perspective on protein folding
    Julia Hockenmaier, Aravind K. Joshi, Ken A. Dill · 2006 · Proteins Structure Function and Bioinformatics
11. A Memetic Algorithm for 3D Protein Structure Prediction Problem
    Leonardo de Lima Corrêa, Bruno Borguesan, Camilo Farfán, Mario Inostroza-Ponta, Márcio Dorn · 2016 · IEEE Transactions on Computational Biology and Bioinformatics
12. Energy landscape and native-state structure of proteins—A simplified model
    Alessandro Flammini, Jayanth R. Banavar, Amos Maritan · 2002 · Europhysics Letters (EPL)
13. Protein Structure Prediction in 1D, 2D, and 3D
    Burkhard Rost · 1998 · Encyclopedia of Computational Chemistry
14. Dynamic Transition from α-Helices to β-Sheets in Polypeptide Coiled-Coil Motifs
    Kirill A. Minin, Artem Andreyevich Zhmurov, Kenneth A. Marx, Prashant K. Purohit, Valeri Abulevich Barsegov · 2017 · Journal of the American Chemical Society
15. Electronic Properties of the Amino Acid Side Chains Contribute to the Structural Preferences in Protein Folding
    D. Dwyer · 2001 · Journal of Biomolecular Structure and Dynamics
16. Relationship between protein structure and geometrical constraints
    Ole Lund, Jan Erik Hansen, Søren Brunak, J. Bohr · 1996 · Protein Science
17. Protein Structural Segments and Their Interconnections Derived from Optical Spectra. Thermal Unfolding of Ribonuclease T1 as an Example
    Petr Pančoška, Heinz Fabian, Gorm Yoder, Vladimı́r Baumruk, Timothy A. Keiderling · 1996 · Biochemistry
18. Building a Better Fragment Library for De Novo Protein Structure Prediction
    Saulo H. P. de Oliveira, Jiye Shi, Charlotte Mary Deane · 2015 · PLoS ONE
19. Circular Dichroism of Protein-Folding Intermediates
    Robert W. Woody · 2004 · Methods in enzymology on CD-ROM/Methods in enzymology
20. Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census
    Mark Gerstein · 1998 · Proteins Structure Function and Bioinformatics
21. Thermodynamic model of secondary structure for α-helical peptides and proteins
    A. Lomize, H. Mosberg · 1997 · Biopolymers
22. Sampling protein conformations using segment libraries and a genetic algorithm
    John R. Gunn · 1997 · The Journal of Chemical Physics
23. ASTRO‐FOLD 2.0: An enhanced framework for protein structure prediction
    A. Subramani, Yinan Wei, Christodoulos A. Floudas · 2011 · AIChE Journal
24. Interhelical Angle and Distance Preferences in Globular Proteins
    Sang‐Yoon Lee, Gregory S. Chirikjian · 2004 · Biophysical Journal
25. Local interactions in a Schellman motif dictate interhelical arrangement in a protein fragment
    Muppalla Sukumar, Lila M. Gierasch · 1997 · Folding and Design
26. Distance geometry generates native‐like folds for small helical proteins using the consensus distances of predicted protein structures
    Enoch S. Huang, Jay W. Ponder, Ram Samudrala · 1998 · Protein Science
27. Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formation
    Richard Bonneau, Charlie E. M. Strauss, David A. Baker · 2001 · Proteins Structure Function and Bioinformatics
28. Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme
    Steven Hayward, Akio Kitao, Herman J. C. Berendsen · 1997 · Proteins Structure Function and Bioinformatics
29. A pentapeptide-based method for protein secondary structure prediction
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30. Ramachandran maps for side chains in globular proteins
    George D. Rose · 2019 · Proteins Structure Function and Bioinformatics
31. Physical‐chemical determinants of turn conformations in globular proteins
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32. Design of an optimal Chebyshev‐expanded discrimination function for globular proteins
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33. Meeting halfway on the bridge between protein folding theory and experiment
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34. Predicting the structures of 18 peptides using Geocore
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35. A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme
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36. β-sheet Topology Prediction with High Precision and Recall for β and Mixed α/β Proteins
    Ashwin Subramani, Christodoulos A. Floudas · 2012 · PLoS ONE
37. Modeling the Early Stages of Phase Separation in Disordered Elastin-like Proteins
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38. Constraint-based assembly of tertiary protein structures from secondary structure elements.
    Kaizhi Yue, Ken A. Dill · 2000 · PubMed Central
39. [2] Modified amino acids as probes of helix stability
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40. Conformation spaces of proteins
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41. The C-terminal Sequence of the Chaperonin GroES Is Required for Oligomerization
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42. Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins
    Konda Mani Saravanan, Samuel Selvaraj · 2017 · Journal of Biological Physics
43. Exploring the effects of hydrogen bonding and hydrophobic interactions on the foldability and cooperativity of helical proteins using a simplified atomic model
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44. The elastic net algorithm and protein structure prediction
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45. Sequential Collapse Model for Protein Folding Pathways
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46. Analysis and algorithms for protein sequence–structure alignment
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47. Protein structure prediction by global energy optimization
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48. Conformational Sampling Techniques
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49. Selecting near‐native conformations in homology modeling: The role of molecular mechanics and solvation terms
    Ajit H. Janardhan, Sándor Vajda · 1998 · Protein Science
50. Modularity in protein structures: study on all-alpha proteins
    Taushif Khan, Indira Ghosh · 2015 · Journal of Biomolecular Structure and Dynamics
51. A hybrid genetic algorithm for the 3-D protein structure prediction problem using a path-relinking strategy
    Márcio Dorn, Luciana Salete Buriol, Luís C. Lamb · 2011 · IEEE Congress on Evolutionary Computation (CEC)
52. Directionality in protein fold prediction
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53. Protein folding by a biased Monte Carlo procedure in the dihedral angle space
    Byungkook Lee, Natalya A. Kurochkina, g Seok Kang · 1996 · The FASEB Journal
54. Structural Features Responsible for the Biological Stability of Histoplasma’s Virulence Factor CBP
    Moriah Rene Beck, Gregory T. DeKoster, David M. Hambly, Michael L. Gross, David P. Cistola, William E. Goldman · 2008 · Biochemistry
55. Diffusive Motions Control the Folding and Unfolding Kinetics of the Apomyoglobin pH 4 Molten Globule Intermediate
    Carlos H.I. Ramos, Sébastien Weisbuch, Marc Jamin · 2007 · Biochemistry
56. An improved hybrid global optimization method for protein tertiary structure prediction
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57. Interaction-based programming with classages
    Yu David Liu, Scott F. Smith · 2005 · Conference on Object-Oriented Programming Systems, Languages, and Applications
58. A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment
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59. Aromatic side‐chain interactions in proteins: Near‐ and far‐sequence Tyr‐X pairs
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60. Reduced Protein Models and their Application to the Protein Folding Problem
    Jeffrey Skolnick, Andrzej Koliński, Ángel R. Ortíz · 1998 · Journal of Biomolecular Structure and Dynamics
61. Equilibrium states of rigid bodies with multiple interaction sites: Application to protein helices
    Burak Erman, İvet Bahar, Robert L. Jernigan · 1997 · The Journal of Chemical Physics
62. Molecular Structure Prediction by Global Optimization
    Ken A. Dill, A. T. Phillips, J. B. Rosen · 1997 · Nonconvex optimization and its applications
63. Monte Carlo Approaches to the Protein Folding Problem
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64. Comparative binding energetics of Mg2+, Ca2+, Zn2+, and Cd2+ to biologically relevant ligands: Combined ab initio SCF supermolecule and molecular mechanics investigation
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65. A3N: An artificial neural network n-gram-based method to approximate 3-D polypeptides structure prediction
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66. Three-dimensional protein structure prediction based on memetic algorithms
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67. Protein structure prediction begins well but ends badly
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68. CGU: An Algorithm for Molecular Structure Prediction
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69. Convergent evolution of protein structure prediction and computer chess tournaments: CASP, Kasparov, and CAFASP
    Naomi Siew, D. Fischer · 2001 · IBM Systems Journal
70. PDZ domain-dependent regulation of NHE3 protein by both internal Class II and C-terminal Class I PDZ-binding motifs
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71. CReF
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72. Analysis of protein contacts into Protein Units
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73. Local sequence information in cellular retinoic acid‐binding protein I: Specific residue roles in β‐turns*
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74. The origami of life
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75. A test of the relationship between sequence and structure in proteins: Excision of the heme binding site in apocytochrome b5
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76. Ab Initio Protein Structure Prediction: Methods and challenges
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77. Distinguishing foldable proteins from nonfolders: When and how do they differ?
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78. Assembly of protein tertiary structures from secondary structures using optimized potentials
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79. Physical–chemical determinants of coil conformations in globular proteins
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80. Conformational search using a molecular dynamics-minimization procedure: Applications to clusters of coulombic charges, Lennard-Jones particles, and waters
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81. Interaction potentials for protein folding
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82. A phosphoinositide-binding sequence is shared by PH domain target molecules—a model for the binding of PH domains to proteins
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83. Exploring the early steps of aggregation of amyloid-forming peptide KFFE
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84. Finding the low-energy forms of avian pancreatic polypeptide with the diffusion-process-controlled Monte Carlo method
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85. A knowledge-based method for protein structure refinement and prediction.
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86. Studies of Early Events of Folding of a Predominately β-Sheet Protein Using Fluorescence Correlation Spectroscopy and Other Biophysical Methods
    Suparna Sarkar, Krishnananda Chattopadhyay · 2014 · Biochemistry
87. Improving Strand Pairing Prediction through Exploring Folding Cooperativity
    Jieun Jeong, Piotr Berman, Teresa M. Przytycka · 2008 · IEEE Transactions on Computational Biology and Bioinformatics
88. The Non-native Helical Intermediate State May Accumulate at Low pH in the Folding and Aggregation Landscape of the Intestinal Fatty Acid Binding Protein
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89. Mining the Protein Data Bank with CReF to predict approximate 3-D structures of polypeptides
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90. A knowledge-based genetic algorithm to predict three-dimensional structures of polypeptides
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91. Protein folding mechanisms and the multidimensional folding funnel
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92. Design of protein function by physical perturbation method
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93. Prediction of Protein Structure Through Evolution
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94. Anisotropic effective interactions in a coarse‐grained tube picture of proteins
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95. The Physical Foundation of Protein Architecture
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96. PHYSICAL FOUNDATION OF PROTEIN ARCHITECTURE
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97. Transient, Highly Populated, Building Blocks Folding Model
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98. Primary structure of the common polypeptide chain b from the multi‐hemoglobin system of the hydrothermal vent tube worm Riftia pachyptila: An insight on the sulfide binding‐site
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99. Strategies for protein folding and design
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100. Bringing Folding Pathways into Strand Pairing Prediction
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