Concepts in protein folding

The protein data bank: A computer-based archival file for macromolecular structures

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,582 · see citing works

Statistical mechanics of chain molecules

Flory, P. J., & Volkenstein, M. V. (1969) · Biopolymers · doi:10.1002/bip.1969.360080514 · Cited by 6,449 · see citing works

Dominant forces in protein folding

Dill, K. A. (1990) · Biochemistry · doi:10.1021/bi00483a001 · Cited by 3,824 · see citing works

The Physics of Rubber Elasticity

Treloar, L. R. G., & Montgomery, D. J. (1959) · Physics Today · doi:10.1063/1.3060678 · Cited by 3,797 · see citing works

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

Bowie, J. U., Lüthy, R., & Eisenberg, D. (1991) · Science · doi:10.1126/science.1853201 · Cited by 2,851 · see citing works

Critical Exponents in 3.99 Dimensions

Wilson, K. G., & Fisher, M. E. (1972) · Physical Review Letters · doi:10.1103/physrevlett.28.240 · Cited by 1,658 · see citing works

The statistical mechanics of polymers with excluded volume

Edwards, S. F. (1965) · Proceedings of the Physical Society · doi:10.1088/0370-1328/85/4/301 · Cited by 1,360 · see citing works

Cold Denaturation of Protein

Privalov, P. L. (1990) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409239009090612 · Cited by 1,074 · see citing works

Calculation of conformational ensembles from potentials of mena force

Sippl, M. J. (1990) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80269-4 · Cited by 1,064 · see citing works

Exponents for the excluded volume problem as derived by the Wilson method

de Gennes, P. G. (1972) · Physics Letters A · doi:10.1016/0375-9601(72)90149-1 · Cited by 1,027 · see citing works

Evidence for a molten globule state as a general intermediate in protein folding

Ptitsyn, O. B., Pain, R. H., Semisotnov, G. V., Žerovnik, E., & RAZGULYAEV, O. I. (1990) · FEBS Letters · doi:10.1016/0014-5793(90)80143-7 · Cited by 678 · see citing works

Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins

Cornette, J. L., Cease, K. B., Margalit, H., Spouge, J. L., Berzofsky, J. A., & DeLisi, C. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90189-6 · Cited by 641 · see citing works

Transient folding intermediates characterized by protein engineering

Matouschek, A. T., Kellis, J. T., Serrano, L. G., Bycroft, M., & Fersht, A. R. (1990) · Nature · doi:10.1038/346440a0 · Cited by 451 · see citing works

Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area

Livingstone, J. R., Spolar, R. S., & Record, M. T. (1991) · Biochemistry · doi:10.1021/bi00231a019 · Cited by 336 · see citing works

Kinetic role of a meta-stable native-like two-disulphide species in the folding transition of bovine pancreatic trypsin inhibitor

Creighton, T. E., & Goldenberg, D. P. (1984) · Journal of Molecular Biology · doi:10.1016/0022-2836(84)90077-9 · Cited by 307 · see citing works

The effects of internal constraints on the configurations of chain molecules

Chan, H. S., & Dill, K. A. (1990) · The Journal of Chemical Physics · doi:10.1063/1.458605 · Cited by 192 · see citing works

Mean-Field Model for Protein Folding

Garel, T., & Orland, H. (1988) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/6/4/005 · Cited by 189 · see citing works

Short range correlation between elements of a long polymer in a good solvent

Cloizeaux, J. D. (1980) · Journal de physique · doi:10.1051/jphys:01980004103022300 · Cited by 182 · see citing works

Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: A prediction of the structure of the catalytic domain of protein kinases

Benner, S. A., & Gerloff, D. L. (1991) · Advances in Enzyme Regulation · doi:10.1016/0065-2571(91)90012-b · Cited by 170 · see citing works

The theory of thermodynamics

Waldram, J. R. (1985) · CERN Document Server (European Organization for Nuclear Research) · Cited by 168 · see citing works

Structure-derived hydrophobic potential

Casari, G., & Sippl, M. J. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90556-y · Cited by 166 · see citing works

A simple statistical field theory of heteropolymer collapse with application to protein folding

Bryngelson, J. D., & Wolynes, P. G. (1990) · Biopolymers · doi:10.1002/bip.360300117 · Cited by 162 · see citing works

Identification of predictive sequence motifs limited by protein structure data base size

Rooman, M. J., & Wodak, S. J. (1988) · Nature · doi:10.1038/335045a0 · Cited by 161 · see citing works

A consistent picture of protein dynamics.

Parak, F., & Knapp, E. (1984) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.81.22.7088 · Cited by 159 · see citing works

A search for the most stable folds of protein chains

Finkelstein, A. V., & Reva, B. A. (1991) · Nature · doi:10.1038/351497a0 · Cited by 136 · see citing works

Dynamical approach study of spurious steady-state numerical solutions of nonlinear differential equations. I. The dynamics of time discretization and its implications for algorithm development in computational fluid dynamics

Yee, H. C., Sweby, P. K., & Griffiths, D. F. (1991) · Journal of Computational Physics · doi:10.1016/0021-9991(91)90001-2 · Cited by 114 · see citing works

Molecular theory of associative memory Hamiltonian models of protein folding

Sasai, M., & Wolynes, P. G. (1990) · Physical Review Letters · doi:10.1103/physrevlett.65.2740 · Cited by 83 · see citing works

Generalized protein tertiary structure recognition using associative memory hamiltonians

Friedrichs, M. S., Goldstein, R. A., & Wolynes, P. G. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90591-s · Cited by 79 · see citing works

Chemical Sequence and Spatial Structure in Simple Models of Biopolymers

Garel, T., & Orland, H. (1988) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/6/7/005 · Cited by 66 · see citing works

Mapping transition states of protein unfolding by protein engineering of ligand-binding sites

Sancho, J., Meiering, E. M., & Fersht, A. R. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)80188-z · Cited by 56 · see citing works

The Reversibility of Protein Coagulation

Anson, M. L., & Mirsky, A. E. (1931) · The Journal of Physical Chemistry · doi:10.1021/j150319a015 · Cited by 46 · see citing works

Coil-globule transition: comparison of field theoretic and conformational space formulations

Kholodenko, A. L., & Freed, K. F. (1984) · Journal of Physics A Mathematical and General · doi:10.1088/0305-4470/17/13/022 · Cited by 45 · see citing works

Bounds for the fractal dimension of space

Schäfer, A., & Müller, B. (1986) · Journal of Physics A Mathematical and General · doi:10.1088/0305-4470/19/18/034 · Cited by 39 · see citing works

Molecular Dynamics Simulation on the Connection Machine

Windemuth, A., & Schulten, K. (1991) · Molecular Simulation · doi:10.1080/08927029108022421 · Cited by 36 · see citing works

Knowledge-based prediction of protein structures

Kaden, F., Koch, I., & Selbig, J. (1990) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(05)80253-x · Cited by 28 · see citing works

The entropic tension of protein loops

Thomas, D. J. (1990) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80334-1 · Cited by 13 · see citing works

Folding pathway enigma

Büchner, J., & Kiefhaber, T. (1990) · Nature · doi:10.1038/343601b0 · Cited by 9 · see citing works

A simplified mechanical model of proteins tested on the globin fold

Thomas, D. J. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90512-5 · Cited by 8 · see citing works

Applying machine learning methods for finding significant amino acid properties in proteins

Selbig, J., Kaden, F., & Koch, I. (1992) · FEBS Letters · doi:10.1016/0014-5793(92)80547-t · Cited by 6 · see citing works

Critical assessment of methods of protein structure prediction (CASP)—Round <scp>XIV</scp>

Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26237 · Cited by 503 · see citing works

Intrinsic Disorder, Protein–Protein Interactions, and Disease

Uversky, V. N. (2017) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2017.06.005 · Cited by 118 · see citing works

A simplified amino acid potential for use in structure predictions of proteins

Wallqvist, A., & Ullner, M. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340180308 · Cited by 78 · see citing works

A computational pathway for bracketing native-like structures for small alpha helical globular proteins

Narang, P., Bhushan, K., Bose, S., & Jayaram, B. (2005) · Physical Chemistry Chemical Physics · doi:10.1039/b502226f · Cited by 68 · see citing works

Protein folding and association: In vitro studies for self-organization and targeting in the cell

Jaenicke, R. (1996) · Current topics in cellular regulation · doi:10.1016/s0070-2137(96)80008-2 · Cited by 62 · see citing works

Towards protein folding by global energy optimization

Abagyan, R. A. (1993) · FEBS Letters · doi:10.1016/0014-5793(93)81406-p · Cited by 42 · see citing works

Circular Dichroism Evidence for the Presence of Burst-Phase Intermediates on the Conformational Folding Pathway of Ribonuclease A

Houry, W. A., Rothwarf, D. M., & Scheraga, H. A. (1996) · Biochemistry · doi:10.1021/bi960617m · Cited by 41 · see citing works

Functional unfoldomics: Roles of intrinsic disorder in protein (multi)functionality

Uversky, V. N. (2023) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2023.11.001 · Cited by 29 · see citing works

Thermodynamics of a molten globule state of human serum albumin by 3-β-hydroxybutyrate as a ketone body

Bohlooli, M., Moosavi‐Movahedi, A. A., Taghavi, F., Habibi-Rezaei, M., Seyedarabi, A., Saboury, A. A., & Ahmad, F. (2012) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2012.12.018 · Cited by 22 · see citing works

Structure and dynamics of the ‘protein folding code’ inferred using Tlusty's topological rate distortion approach

Wallace, R. (2010) · Biosystems · doi:10.1016/j.biosystems.2010.09.007 · Cited by 13 · see citing works

On “Levinthal paradox” and the theory of protein folding

Durup, J. (1998) · Journal of Molecular Structure THEOCHEM · doi:10.1016/s0166-1280(97)00238-8 · Cited by 9 · see citing works

A small modified hammerhead ribozyme and its conformational characteristics determined by mutagenesis and lattice calculation

Lustig, B., Lin, N., Smith, S. M., Jernigan, R. L., & Jeang, K. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.17.3531 · Cited by 6 · see citing works

Classical and modern differential scanning calorimetry of proteins: Integrating equilibrium thermodynamics with emerging diagnostic and pharmaceutical applications

Bohlooli, M., Saboury, A. A., Ghaffari‐Moghaddam, M., Khajeh, M., & Şenol, H. (2026) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2026.03.007 · Cited by 1 · see citing works

Do the hemeproteins behave as a dissipative structure?

Alpert, B., Tilly, V. L., Pin, S., Sire, O., & Zentz, C. (1996) · International Journal of Quantum Chemistry · doi:10.1002/(sici)1097-461x(1996)59:4 · Cited by 1 · see citing works

Learning molecular traits of human pain disease via voltage-gated sodium channel structure renormalization

Xenakis, M. N., & Lampert, A. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.11.048

Can a Protein Compute Its Fold? A Review of Information-Theoretic and Computational PerspectivesPreprint

Todd, I. (2025) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.15540906

The protein folding problem

Janković, B. G., & Polović, N. (2017) · doi:10.5281/zenodo.827150 · Cited by 3 · see citing works

Molecular mechanics work station for protein conformational studies

Fine, R., Levinthal, C., SCHOENBORN, B. P., Dimmier, G., & Rankowitz, C. (1984) · University of North Texas Digital Library (University of North Texas)

Version 2 Protein folding disorders: Toward a basic biological paradigm

Rodrick Wallace Ph., D. (2010)

De novo protein folding on computers. Benefits and challenges

Robson, B. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.105292 · Cited by 21 · see citing works