We review several results related to the protein folding problem. We start by analyzing the nature of the interactions among protein atoms and their influence on folding. We then examine several approaches to solve the folding problem, or restricted versions thereof. We conclude with a survey of results related to the computational complexity of the protein folding problem and analyze their implications on finding efficient solutions to the problem. 1
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338
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Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
– Kabsch, Sander
- 1983
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98
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Principles that govern folding of protein chains
– Anfinsen
- 1973
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60
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Theory for the folding and stability of globular proteins
– Dill
- 1985
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50
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Moult J: Finding the lowest Free-Energy Conformation of a protein is an NP-hard problem – Proof and Implications
– Unger
- 1993
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49
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Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal
– Hart, Istrail
- 1995
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48
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An empirical energy function for threading protein sequence through the folding motif. Proteins
– Bryant, Lawrence
- 1993
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44
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Dominant forces in protein folding
– Dill
- 1990
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43
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The protein threading problem with sequence amino acid interaction preferences is NP-complete
– Lathrop
- 1994
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39
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A simplified representation of protein conformations for rapid simulation of protein folding
– Levitt
- 1976
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36
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Proteins : Structures and molecular properties
– Creighton
- 1993
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33
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How does a protein fold
– Sali, Shakhnovich, et al.
- 1994
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32
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AMBER: Assisted model building with energy refinement. a general program for modeling molecules and their interactions
– Weiner, Kollman
- 1981
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30
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Complexity of protein folding
– Fraenkel
- 1993
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29
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An all atom force field for simulations of proteins and nucleic acids
– Weiner, Kollman, et al.
- 1986
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22
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Prediction of protein side-chain conformation by packing optimization
– Lee, Subbiah
- 1991
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22
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LINUS-A hierarchic procedure to predict the fold of a protein. Protein.i
– Srinivasan, Rose
- 1995
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17
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Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors
– Holm, Sander
- 1991
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17
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A new approach to the rapid determination of protein side-chain conformations
– Tuffery, Etchebest, et al.
- 1991
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14
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A branch-and-bound algorithm for optimal protein threading with pairwise (contact potential) amino acid interactions
– Lathrop, Smith
- 1994
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14
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Stereochemistry of polypeptide chain configurations
– Ramachandran, Ramakrishnan, et al.
- 1963
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12
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Computational complexity, protein structure prediction, and the levinthal paradox
– Ngo, Marks, et al.
- 1994
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8
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Hierarchic organization of domains in globular proteins
– Rose
- 1979
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6
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Hydrogen bonding in globular proteins
– Stickle, Presta, et al.
- 1992
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6
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Conformational energy calculations on polypeptides and proteins
– V'asquez, N'emethy, et al.
- 1994
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5
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The effects of internal constraints on the configurations of chain molecules
– Chan, Dill
- 1990
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4
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On the calculation of electrostatic interactions in proteins
– Gilson, Rashin, et al.
- 1985
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3
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Thermal stabilities of globular proteins
– Dill, Alonso, et al.
- 1989
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3
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Hydrogen bonding, hydrophobicity, packing, and protein folding
– Rose, Wolfenden
- 1993
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3
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Levinthal's paradox
– Zwanzig, Szabo
- 1992
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2
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White jr. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain
– Anfinsen, Haber, et al.
- 1961
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2
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Treatment of electrostatic effects in macromolecular modelling
– Harvey
- 1989
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2
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Protein folding -- what's the question
– Lattman, Rose
- 1993
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2
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and Arieh Warshel. Computer Simulation of Protein Folding
– Levitt
- 1975
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1
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Simulating the folding of small proteins by use of the local minimum energy and the free solvation energy yields native-like structures
– Brasseur
- 1995
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1
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Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination: A model study of crambin
– Clore, Brunger, et al.
- 1986
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1
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Chemistry at HARvard Macromolecular Mechanics, 24b1 edition
– College
- 1995
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1
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A Midas Tutorial
– Glasfeld
- 1996
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1
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The hydrophobic effect in protein folding
– Lins, Brasseur
- 1995
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