Heteropolymer freezing and design: Towards physical models of protein folding

Principles of polymer chemistry

(1995) · Choice Reviews Online · doi:10.5860/choice.33-2140 · Cited by 15,292 · see citing works

<i>Scaling Concepts in Polymer Physics</i>

de Gennes, P. G., & Witten, T. A. (1980) · Physics Today · doi:10.1063/1.2914118 · Cited by 9,348 · see citing works

The theory of polymer dynamics

Doi, M., & Edwards, S. F. (1986) · Cited by 8,964 · see citing works

The Neutral Theory of Molecular Evolution

Kimura, M. (1979) · Scientific American · doi:10.1038/scientificamerican1179-98 · Cited by 7,698 · see citing works

Principles that Govern the Folding of Protein Chains

Anfinsen, C. B. (1973) · Science · doi:10.1126/science.181.4096.223 · Cited by 7,096 · 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

Spin glasses: Experimental facts, theoretical concepts, and open questions

Binder, K., & Young, A. P. (1986) · Reviews of Modern Physics · doi:10.1103/revmodphys.58.801 · Cited by 5,134 · see citing works

Spin Glass Theory and Beyond

Mézard, M., Giorgio Parisi, A., VIRASORO, M. A., & Thouless, D. J. (1988) · Physics Today · doi:10.1063/1.2811676 · Cited by 2,683 · see citing works

Lectures On Phase Transitions And The Renormalization Group

Goldenfeld, N. (1972) · CRC Press eBooks · doi:10.1201/9780429493492 · Cited by 2,654 · see citing works

Funnels, pathways, and the energy landscape of protein folding: A synthesis

Bryngelson, J. D., Onuchic, J. N., Socci, N. D., & Wolynes, P. G. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340210302 · Cited by 2,648 · see citing works

From Levinthal to pathways to funnels

Dill, K. A., & Chan, H. S. (1997) · Nature Structural &amp; Molecular Biology · doi:10.1038/nsb0197-10 · Cited by 2,293 · see citing works

Stability of Proteins Small Globular Proteins

Privalov, P. L. (1979) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60460-x · Cited by 2,163 · see citing works

Protein Denaturation

Tanford, C. (1968) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60401-5 · Cited by 2,135 · see citing works

Statistical Physics of Macromolecules

Grosberg, A. Y., Khokhlov, A. R., Stanley, H. E., et al. (1995) · Computers in Physics · doi:10.1063/1.4823390 · Cited by 1,683 · see citing works

Spin glasses and the statistical mechanics of protein folding.

Bryngelson, J. D., & Wolynes, P. G. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.21.7524 · Cited by 1,647 · see citing works

Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

Miyazawa, S., & Jernigan, R. L. (1985) · Macromolecules · doi:10.1021/ma00145a039 · Cited by 1,588 · see citing works

Protein Folding

Creighton, T. E. (1992) · Cited by 1,572 · see citing works

The molten globule state as a clue for understanding the folding and cooperativity of globular‐protein structure

Kuwajima, K. (1989) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340060202 · Cited by 1,440 · see citing works

Monte Carlo and Molecular Dynamics Simulations in Polymer Science

Binder, K. (1995) · doi:10.1093/oso/9780195094381.001.0001 · Cited by 1,263 · see citing works

Molten Globule and Protein Folding

Ptitsyn, O. B. (1995) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60546-x · Cited by 1,222 · see citing works

De Novo Protein Design: Fully Automated Sequence Selection

Dahiyat, B. I., & Mayo, S. L. (1997) · Science · doi:10.1126/science.278.5335.82 · Cited by 1,142 · see citing works

Navigating the folding routes

Wolynes, P., Onuchic, J., & Thirumalai, D. (1995) · Science · doi:10.1126/science.7886447 · Cited by 1,080 · see citing works

Computer simulation of protein folding

Levitt, M., & Warshel, A. (1975) · Nature · doi:10.1038/253694a0 · Cited by 1,051 · see citing works

A lattice statistical mechanics model of the conformational and sequence spaces of proteins

Lau, K. F., & Dill, K. A. (1989) · Macromolecules · doi:10.1021/ma00200a030 · Cited by 954 · see citing works

Protein folding funnels: a kinetic approach to the sequence-structure relationship.

Leopold, P., Montal, M., & Onuchic, J. N. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.18.8721 · Cited by 929 · see citing works

Statistical mechanics of neural networks near saturation

Amit, D. J., Gutfreund, H., & Sompolinsky, H. (1987) · Annals of Physics · doi:10.1016/0003-4916(87)90092-3 · Cited by 843 · see citing works

Theoretical Studies of Protein Folding

Gō, N. (1983) · Annual Review of Biophysics and Bioengineering · doi:10.1146/annurev.bb.12.060183.001151 · Cited by 833 · see citing works

Random-Energy Model: Limit of a Family of Disordered Models

Derrida, B. (1980) · Physical Review Letters · doi:10.1103/physrevlett.45.79 · Cited by 821 · see citing works

Intermediates and barrier crossing in a random energy model (with applications to protein folding)

Bryngelson, J. D., & Wolynes, P. G. (1989) · The Journal of Physical Chemistry · doi:10.1021/j100356a007 · Cited by 746 · see citing works

The Protein Data Bank

Abola, E. E., Bernstein, F. C., & Koetzle, T. F. (1984) · Springer eBooks · doi:10.1007/978-1-4899-0375-4_26 · Cited by 739 · see citing works

Some problems of the statistical physics of polymer chains with volume interaction

Lifshitz, I. M., Grosberg, A. Y., & Khokhlov, A. R. (1978) · Reviews of Modern Physics · doi:10.1103/revmodphys.50.683 · Cited by 737 · see citing works

STUDIES ON PROTEIN FOLDING, UNFOLDING AND FLUCTUATIONS BY COMPUTER SIMULATION

Taketomi, H., Ueda, Y., & Gō, N. (1975) · International journal of peptide & protein research · doi:10.1111/j.1399-3011.1975.tb02465.x · Cited by 679 · see citing works

Emergence of Preferred Structures in a Simple Model of Protein Folding

Li, H., Helling, R. C., Tang, C., & Wingreen, N. S. (1996) · Science · doi:10.1126/science.273.5275.666 · Cited by 650 · see citing works

Characterization of a Helical Protein Designed from First Principles

Regan, L., & DeGrado, W. F. (1988) · Science · doi:10.1126/science.3043666 · Cited by 543 · see citing works

Toward an outline of the topography of a realistic protein-folding funnel.

Onuchic, J. N., Wolynes, P. G., Luthey-Schulten, Z., & Socci, N. D. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.8.3626 · Cited by 523 · see citing works

On the Structure of Native, Denatured, and Coagulated Proteins

Mirsky, A. E., & Pauling, L. C. (1936) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.22.7.439 · Cited by 521 · see citing works

Engineering of stable and fast-folding sequences of model proteins.

Shakhnovich, E. I., & Gutin, A. M. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.15.7195 · Cited by 516 · see citing works

Diffusive dynamics of the reaction coordinate for protein folding funnels

Socci, N. D., Onuchic, J. N., & Wolynes, P. G. (1996) · The Journal of Chemical Physics · doi:10.1063/1.471317 · Cited by 504 · see citing works

On the transition coordinate for protein folding

Du, R., Pande, V. S., Grosberg, A. Y., Tanaka, T., & Shakhnovich, E. I. (1998) · The Journal of Chemical Physics · doi:10.1063/1.475393 · Cited by 486 · see citing works

Specific Nucleus as the Transition State for Protein Folding: Evidence from the Lattice Model

Abkevich, V., Gutin, A. M., & Shakhnovich, E. I. (1994) · Biochemistry · doi:10.1021/bi00199a029 · Cited by 477 · see citing works

Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications.

Fersht, A. R. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.24.10869 · Cited by 473 · see citing works

The role of topological constraints in the kinetics of collapse of macromolecules

Grosberg, A. Y., Nechaev, S. K., & Shakhnovich, E. I. (1988) · Journal de physique · doi:10.1051/jphys:0198800490120209500 · Cited by 437 · see citing works

The denatured state (the other half of the folding equation) and its role in protein stability

Shortle, D. (1996) · The FASEB Journal · doi:10.1096/fasebj.10.1.8566543 · Cited by 405 · see citing works

Theory of polyampholyte solutions

Higgs, P. G., & Joanny, J. (1991) · The Journal of Chemical Physics · doi:10.1063/1.460012 · Cited by 397 · see citing works

First-Principles Calculation of the Folding Free Energy of a Three-Helix Bundle Protein

Boczko, E. M., & Brooks, C. L. (1995) · Science · doi:10.1126/science.7618103 · Cited by 394 · see citing works

Proteins with selected sequences fold into unique native conformation

Shakhnovich, E. I. (1994) · Physical Review Letters · doi:10.1103/physrevlett.72.3907 · Cited by 393 · see citing works

De Novo Design, Expression, and Characterization of Felix: a Four-Helix Bundle Protein of Native-Like Sequence

Hecht, M. H., Richardson, J. S., Richardson, D. C., & Ogden, R. C. (1990) · Science · doi:10.1126/science.2392678 · Cited by 391 · see citing works

Theoretical studies of protein-folding thermodynamics and kinetics

Shakhnovich, E. I. (1997) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(97)80005-x · Cited by 379 · see citing works

Validity of the “two‐state” hypothesis for conformational transitions of proteins

Lumry, R. W., Biltonen, R. L., & Brandts, J. F. (1966) · Biopolymers · doi:10.1002/bip.1966.360040808 · Cited by 359 · see citing works

Kinetics and thermodynamics of folding in model proteins.

Camacho, C. J., & Thirumalai, D. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.13.6369 · Cited by 357 · see citing works

Optimal protein-folding codes from spin-glass theory.

Goldstein, R. A., Luthey-Schulten, Z. A., & Wolynes, P. G. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.11.4918 · Cited by 351 · see citing works

Protein folding funnels: the nature of the transition state ensemble

Onuchic, J. N., Socci, N. D., Luthey-Schulten, Z. A., & Wolynes, P. G. (1996) · Folding and Design · doi:10.1016/s1359-0278(96)00060-0 · Cited by 330 · see citing works

Formation of unique structure in polypeptide chains

Shakhnovich, E. I., & Gutin, A. M. (1989) · Biophysical Chemistry · doi:10.1016/0301-4622(89)80058-4 · Cited by 321 · see citing works

Polymer Principles in Protein Structure and Stability

Chan, H. S., & Dill, K. A. (1991) · Annual Review of Biophysics and Biophysical Chemistry · doi:10.1146/annurev.bb.20.060191.002311 · Cited by 308 · see citing works

The Protein Folding Problem

Chan, H. S., & Dill, K. A. (1993) · Physics Today · doi:10.1063/1.881371 · Cited by 308 · see citing works

Protein design automation

Dahiyat, B. I., & Mayo, S. L. (1996) · Protein Science · doi:10.1002/pro.5560050511 · Cited by 298 · see citing works

Folding kinetics of proteinlike heteropolymers

Socci, N. D., & Onuchic, J. N. (1994) · The Journal of Chemical Physics · doi:10.1063/1.467775 · Cited by 297 · see citing works

Monte carlo simulations of protein folding. I. Lattice model and interaction scheme

Koliński, A., & Skolnick, J. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340180405 · Cited by 295 · see citing works

Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first‐order phase transition

Shakhnovich, E. I., & Finkelstein, A. V. (1989) · Biopolymers · doi:10.1002/bip.360281003 · Cited by 290 · see citing works

A test of lattice protein folding algorithms.

Yue, K., Fiebig, K. M., Thomas, P. D., Chan, H. S., Shakhnovich, E. I., & Dill, K. A. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.1.325 · Cited by 286 · see citing works

How to Derive a Protein Folding Potential? A New Approach to an Old Problem

Mirny, L. A., & Shakhnovich, E. I. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0704 · Cited by 277 · see citing works

Enumeration of all compact conformations of copolymers with random sequence of links

Shakhnovich, E. I., & Gutin, A. M. (1990) · The Journal of Chemical Physics · doi:10.1063/1.459480 · Cited by 259 · see citing works

An iterative method for extracting energy-like quantities from protein structures.

Thomas, P. D., & Dill, K. A. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.21.11628 · Cited by 254 · see citing works

Pathways for protein folding: is a new view needed?

Pande, V. S., Grosberg, A. Y., Tanaka, T., & Rokhsar, D. S. (1998) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(98)80012-2 · Cited by 252 · see citing works

Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2.

Li, A., & Daggett, V. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.22.10430 · Cited by 248 · see citing works

A generalization of the Random Energy Model which includes correlations between energies

Derrida, B. (1985) · Journal de Physique Lettres · doi:10.1051/jphyslet:01985004609040100 · Cited by 239 · see citing works

Statistical physics of polymer gels

Panyukov, S., & Rabin, Y. (1996) · Physics Reports · doi:10.1016/0370-1573(95)00068-2 · Cited by 238 · see citing works

The complexity and accuracy of discrete state models of protein structure

Park, B. H., & Levitt, M. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0311 · Cited by 232 · see citing works

Quantum noise in photonics

HENRY, C. H., & Kazarinov, R. F. (1996) · Reviews of Modern Physics · doi:10.1103/revmodphys.68.801 · Cited by 220 · see citing works

Biomolecules: Where the Physics of Complexity and Simplicity Meet

Frauenfelder, H., & Wolynes, P. G. (1994) · Physics Today · doi:10.1063/1.881414 · Cited by 217 · see citing works

Why do protein architectures have boltzmann‐like statistics?

Finkelstein, A. V., Badretdinov, A. Y., & Gutin, A. M. (1995) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340230204 · Cited by 200 · see citing works

Criterion that Determines the Foldability of Proteins

Klimov, D. K., & Thirumalai, D. (1996) · Physical Review Letters · doi:10.1103/physrevlett.76.4070 · Cited by 197 · see citing works

A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins

Koliński, A., Godzik, A., & Skolnick, J. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464706 · Cited by 193 · 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

PROTEIN FOLDING: The Endgame

Levitt, M., Gerstein, M., Huang, E. S., Subbiah, S., & Tsai, J. W. (1997) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.66.1.549 · Cited by 189 · see citing works

Equilibrium swelling properties of polyampholytic hydrogels

English, A. E., Mafé, S., Manzanares, J. A., et al. (1996) · The Journal of Chemical Physics · doi:10.1063/1.471560 · Cited by 188 · see citing works

Noninteracting local‐structure model of folding and unfolding transition in globular proteins. II. Application to two‐dimensional lattice proteins

Abe, H., & Gō, N. (1981) · Biopolymers · doi:10.1002/bip.1981.360200512 · Cited by 184 · see citing works

De novo design of the hydrophobic core of ubiquitin

Lazar, G. A., Desjarlais, J. R., & Handel, T. M. (1997) · Protein Science · doi:10.1002/pro.5560060605 · Cited by 184 · see citing works

How evolution makes proteins fold quickly

Mirny, L. A., Abkevich, V., & Shakhnovich, E. I. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.9.4976 · Cited by 183 · see citing works

Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique

Socci, N. D., & Onuchic, J. N. (1995) · The Journal of Chemical Physics · doi:10.1063/1.470610 · Cited by 180 · see citing works

First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model

Zhou, Y., Hall, C. K., & Karplus, M. (1996) · Physical Review Letters · doi:10.1103/physrevlett.77.2822 · Cited by 179 · see citing works

Molecular Dynamics Simulations of the Unfolding of Barnase in Water and 8 M Aqueous Urea

Tirado‐Rives, J., Orozco, M., & Jorgensen, W. L. (1997) · Biochemistry · doi:10.1021/bi970096i · Cited by 179 · see citing works

The molten globule is a third thermodynamical state of protein molecules

Ptitsyn, O. B., & Uversky, V. N. (1994) · FEBS Letters · doi:10.1016/0014-5793(94)80231-9 · Cited by 178 · see citing works

Quantitative theory of the globule-to-coil transition. 1. Link density distribution in a globule and its radius of gyration

Grosberg, A. Y., & Kuznetsov, D. V. (1992) · Macromolecules · doi:10.1021/ma00033a022 · Cited by 177 · see citing works

Kinetics and Thermodynamics of Folding of ade NovoDesigned Four-helix Bundle Protein

Guo, Z., & Thirumalai, D. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0578 · Cited by 169 · see citing works

A model of the molten globule state from molecular dynamics simulations.

Daggett, V., & Levitt, M. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.11.5142 · Cited by 163 · see citing works

Solution of the generalised random energy model

Derrida, B., & Gardner, E. (1986) · Journal of Physics C Solid State Physics · doi:10.1088/0022-3719/19/13/015 · Cited by 162 · see citing works

Molecular dynamics simulation of protein denaturation:solvation of the hydrophobic cores and secondary structure ofbarnase.

Caflisch, A., & Karplus, M. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.5.1746 · Cited by 162 · see citing works

Instabilities of charged polyampholytes

Kantor, Y., & Mehran Kardar, A. (1995) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.51.1299 · Cited by 158 · see citing works

Structural energetics of the molten globule state

Haynie, D. T., & Freire, E. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340160202 · Cited by 156 · see citing works

Exploring conformational space with a simple lattice model for protein structure

Hinds, D. A., & Levitt, M. (1994) · Journal of Molecular Biology · doi:10.1016/0022-2836(94)90040-x · Cited by 153 · see citing works

Toward Protein Tertiary Structure Recognition by Means of Associative Memory Hamiltonians

Friedrichs, M. S., & Wolynes, P. G. (1989) · Science · doi:10.1126/science.246.4928.371 · Cited by 148 · see citing works

Statistical mechanics of a correlated energy landscape model for protein folding funnels

Plotkin, S. S., Wang, J., & Wolynes, P. G. (1997) · The Journal of Chemical Physics · doi:10.1063/1.473355 · Cited by 147 · see citing works

Frozen states of a disordered globular heteropolymer

Shakhnovich, E. I., & Gutin, A. M. (1989) · Journal of Physics A Mathematical and General · doi:10.1088/0305-4470/22/10/019 · Cited by 146 · see citing works

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

Godzik, A., Skolnick, J., & Koliński, A. (1995) · Protein Science · doi:10.1002/pro.5560041016 · Cited by 144 · see citing works

Evolution-like selection of fast-folding model proteins.

Gutin, A. M., Abkevich, V., & Shakhnovich, E. I. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.5.1282 · Cited by 141 · see citing works

Protein-like copolymers: computer simulation

Khokhlov, A. R., & Khalatur, P. G. (1998) · Physica A Statistical Mechanics and its Applications · doi:10.1016/s0378-4371(97)00473-1 · Cited by 140 · see citing works

Monte Carlo and Molecular Dynamics Simulations

Clementi, E., Corongiu, G., Aida, M., Niesar, U., & Kneller, G. R. (1990) · Springer eBooks · doi:10.1007/978-94-009-2219-8_17 · Cited by 139 · see citing works

Why are some proteins structures so common?

Govindarajan, S., & Goldstein, R. A. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.8.3341 · Cited by 135 · see citing works

Cooperativity in protein folding: from lattice models with sidechains to real proteins

Klimov, D., & Thirumalai, D. (1998) · Folding and Design · doi:10.1016/s1359-0278(98)00018-2 · Cited by 129 · see citing works

Random and Alternating Polyampholytes

Wittmer, J. P., Johner, A., & Joanny, J. (1993) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/24/4/005 · Cited by 128 · see citing works

New Algorithm for Protein Design

Deutsch, J. M., & Kurosky, T. (1996) · Physical Review Letters · doi:10.1103/physrevlett.76.323 · Cited by 127 · see citing works

Statistical mechanics of simple models of protein folding and design

Pande, V. S., Grosberg, A. Y., & Tanaka, T. (1997) · Biophysical Journal · doi:10.1016/s0006-3495(97)78345-0 · Cited by 125 · see citing works

Phase diagram of random copolymers

Sfatos, C. D., Gutin, A. M., & Shakhnovich, E. I. (1993) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.48.465 · Cited by 117 · see citing works

Factors governing the foldability of proteins

Klimov, D. K., & Thirumalai, D. (1996) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(199612)26:4 · Cited by 115 · see citing works

Nonrandomness in protein sequences: evidence for a physically driven stage of evolution?

Pande, V. S., Grosberg, A. Y., & Tanaka, T. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.26.12972 · Cited by 111 · see citing works

Designing amino acid sequences to fold with good hydrophobic cores

Sun, S., Brem, R. B., Chan, H. S., & Dill, K. A. (1995) · Protein Engineering Design and Selection · doi:10.1093/protein/8.12.1205 · Cited by 109 · see citing works

Sequence-structure relationships in proteins and copolymers

Yue, K., & Dill, K. A. (1993) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.48.2267 · Cited by 108 · see citing works

Analysis of topological and nontopological structural similarities in the PDB: New examples with old structures

Alexandrov, N. N., & Fischer, D. (1996) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(199607)25:3 · Cited by 107 · see citing works

Aqueous solution properties of ampholytic copolymers prepared in microemulsions

Corpart, J., & Candau, F. (1993) · Macromolecules · doi:10.1021/ma00058a023 · Cited by 106 · see citing works

Phase diagram of a semiflexible polymer chain in a θ solvent: Application to protein folding

Doniach, S., Garel, T., & Orland, H. (1996) · The Journal of Chemical Physics · doi:10.1063/1.472031 · Cited by 106 · see citing works

Evidence for nonrandom hydrophobicity structures in protein chains.

Irbäck, A., Peterson, C., & Potthast, F. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.18.9533 · Cited by 103 · see citing works

Is the molten globule a third phase of proteins?

Pande, V. S., & Rokhsar, D. S. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.4.1490 · Cited by 103 · see citing works

Fast-folding eriments and the topography of protein folding energy landscapes

Wolynes, P. G., Luthey-Schulten, Z. A., & Onuchic, J. N. (1996) · Chemistry & Biology · doi:10.1016/s1074-5521(96)90090-3 · Cited by 98 · see citing works

Correlated energy landscape model for finite, random heteropolymers

Plotkin, S. S., Wang, J., & Wolynes, P. G. (1996) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.53.6271 · Cited by 93 · see citing works

Optimal Protein Design Procedure

Seno, F., Vendruscolo, M., Maritan, A., & Banavar, J. R. (1996) · Physical Review Letters · doi:10.1103/physrevlett.77.1901 · Cited by 91 · see citing works

Thermodynamic procedure to synthesize heteropolymers that can renature to recognize a given target molecule.

Pande, V. S., Grosberg, A. Y., & Tanaka, T. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.26.12976 · Cited by 87 · see citing works

Why are the same protein folds used to perform different functions?

Finkelstein, A. V., Gutun, A. M., & Badretdinov, A. Y. (1993) · FEBS Letters · doi:10.1016/0014-5793(93)81407-q · Cited by 86 · see citing works

Nucleation mechanism for protein folding and theoretical predictions for hydrogen‐exchange labeling experiments

Thirumalai, D., & Guo, Z. (1995) · Biopolymers · doi:10.1002/bip.360350114 · Cited by 85 · 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

Phase changes in polyampholytes

Edwards, S. F., King, P., & Pincus, P. A. (1980) · Ferroelectrics · doi:10.1080/00150198008209479 · Cited by 81 · see citing works

Statistical mechanics of polyampholytes

Kantor, Y., Kardar, M., & Li, H. (1994) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.49.1383 · Cited by 81 · see citing works

Physical Approaches to Biological Evolution

Volkenstein, M. V. (1994) · Springer eBooks · doi:10.1007/978-3-642-78788-1 · Cited by 80 · see citing works

The foldability landscape of model proteins

Govindarajan, S., & Goldstein, R. A. (1997) · Biopolymers · doi:10.1002/(sici)1097-0282(19971005)42:4 · Cited by 77 · see citing works

Ground state of random copolymers and the discrete random energy model

Gutin, A. M., & Shakhnovich, E. I. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464522 · Cited by 76 · see citing works

Protein Structures and Neutral Theory of Evolution

Ptitsyn, O. B., & Volkenstein, M. V. (1986) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.1986.10507651 · Cited by 76 · see citing works

Statistical mechanics of proteins with ‘‘evolutionary selected’’ sequences

Ramanathan, S., & Shakhnovich, E. I. (1994) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.50.1303 · Cited by 75 · see citing works

All-or-none solvent-induced transitions between native, molten globule and unfolded states in globular proteins

Uversky, V. N., & Ptitsyn, O. B. (1996) · Folding and Design · doi:10.1016/s1359-0278(96)00020-x · Cited by 72 · see citing works

Modelling protein folding: the beauty and power of simplicity

Shakhnovich, E. I. (1996) · Folding and Design · doi:10.1016/s1359-0278(96)00027-2 · Cited by 69 · see citing works

How accurate must potentials be for successful modeling of protein folding?

Pande, V. S., Grosberg, A. Y., & Tanaka, T. (1995) · The Journal of Chemical Physics · doi:10.1063/1.470009 · Cited by 67 · 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

Enumerations of the Hamiltonian walks on a cubic sublattice

Pande, V. S., Joerg, C., Grosberg, A. Y., et al. (1994) · Journal of Physics A Mathematical and General · doi:10.1088/0305-4470/27/18/030 · Cited by 65 · see citing works

Design of proteins with selected thermal properties

Morrissey, M., & Shakhnovich, E. I. (1996) · Folding and Design · doi:10.1016/s1359-0278(96)00054-5 · Cited by 63 · see citing works

Protein structure: what is it possible to predict now?

Finkelstein, A. V. (1997) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(97)80008-5 · Cited by 62 · see citing works

Helix-Coil, Liquid Crystal, and Spin Glass Transitions of a Collapsed Heteropolymer

Luthey-Schulten, Z. A., Ramirez, B. E., & Wolynes, P. G. (1995) · The Journal of Physical Chemistry · doi:10.1021/j100007a057 · Cited by 58 · see citing works

Properties and origins of protein secondary structure

Socci, N. D., Bialek, W., & Onuchic, J. N. (1994) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.49.3440 · Cited by 57 · see citing works

Phase diagram of a model protein derived by exhaustive enumeration of the conformations

Dinner, A. R., Šali, A., Karplus, M., et al. (1994) · The Journal of Chemical Physics · doi:10.1063/1.467769 · Cited by 55 · see citing works

Statistical Mechanics, Protein Structure, and Protein Substrate Interactions

(1994) · NATO ASI series. Series B : Physics · doi:10.1007/978-1-4899-1349-4 · Cited by 53 · see citing works

Partially Folded States of Proteins: Characterization by X-ray Scattering

Doniach, S., Bascle, J., Garel, T., et al. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0668 · Cited by 53 · see citing works

Randomly charged polymers: An exact enumeration study

Kantor, Y., & Mehran Kardar, A. (1995) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.52.835 · Cited by 52 · see citing works

Magnetic properties and the function q(x) of the generalised random-energy model

Derrida, B., & Gardner, E. (1986) · Journal of Physics C Solid State Physics · doi:10.1088/0022-3719/19/29/005 · Cited by 51 · see citing works

Freezing transition of random heteropolymers consisting of an arbitrary set of monomers

Pande, V. S., Grosberg, A. Y., & Tanaka, T. (1995) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.51.3381 · Cited by 50 · see citing works

On the theory of folding kinetics for short proteins

Pande, V. S., Grosberg, A. Y., & Tanaka, T. (1997) · Folding and Design · doi:10.1016/s1359-0278(97)00015-1 · Cited by 47 · see citing works

Is Heteropolymer Freezing Well Described by the Random Energy Model?

Pande, V. S., Grosberg, A. Y., Joerg, C., & Tanaka, T. (1996) · Physical Review Letters · doi:10.1103/physrevlett.76.3987 · Cited by 47 · see citing works

Protein Design in a Lattice Model of Hydrophobic and Polar Amino Acids

Micheletti, C., Seno, F., Maritan, A., & Banavar, J. R. (1998) · Physical Review Letters · doi:10.1103/physrevlett.80.2237 · Cited by 46 · see citing works

Phase Diagram of Heteropolymers with an Imprinted Conformation

Pande, V. S., Grosberg, A. Y., & Tanaka, T. (1995) · Macromolecules · doi:10.1021/ma00111a016 · Cited by 45 · see citing works

When is a potential accurate enough for structure prediction? Theory and application to a random heteropolymer model of protein folding

Bryngelson, J. D. (1994) · The Journal of Chemical Physics · doi:10.1063/1.467114 · Cited by 43 · see citing works

Computer modeling and folding of four‐helix bundles

Rey, A., & Skolnick, J. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340160103 · Cited by 43 · see citing works

How the first biopolymers could have evolved.

Abkevich, V., Gutin, A. M., & Shakhnovich, E. I. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.2.839 · Cited by 42 · see citing works

Proteins from Scratch

DeGrado, W. F. (1997) · Science · doi:10.1126/science.278.5335.80 · Cited by 41 · see citing works

Domains in folding of model proteins

Abkevich, V., Gutin, A. M., & Shakhnovich, E. I. (1995) · Protein Science · doi:10.1002/pro.5560040615 · Cited by 41 · see citing works

Protein folding from a combinatorial perspective

Sauer, R. T. (1996) · Folding and Design · doi:10.1016/s1359-0278(96)00015-6 · Cited by 40 · see citing works

[THE THEORY OF HELIX-COIL TRANSITIONS IN MACROMOLECULES].

Ptitsyn, O. B., & EIZNER, I. E. (1965) · PubMed · Cited by 37 · see citing works

Molecular dynamics simulations of apocytochrome b562– the highly ordered limit of molten globules

Laidig, K. E., & Daggett, V. (1996) · Folding and Design · doi:10.1016/s1359-0278(96)00049-1 · Cited by 36 · see citing works

Statistical mechanics of polymers with distance constraints

Gutin, A. M., & Shakhnovich, E. I. (1994) · The Journal of Chemical Physics · doi:10.1063/1.467193 · Cited by 35 · see citing works

Stability Threshold as a Selection Principle for Protein Design

Vendruscolo, M., Maritan, A., & Banavar, J. R. (1997) · Physical Review Letters · doi:10.1103/physrevlett.78.3967 · Cited by 35 · see citing works

Protein-like copolymers: Computer simulation

Khalatur, P. G., Иванов, В. А., Shusharina, N., & Khokhlov, A. R. (1998) · Russian Chemical Bulletin · doi:10.1007/bf02498152 · Cited by 33 · see citing works

Freezing Transition of Compact Polyampholytes

Pande, V. S., Grosberg, A. Y., Joerg, C., et al. (1996) · Physical Review Letters · doi:10.1103/physrevlett.77.3565 · Cited by 30 · see citing works

Thermodynamics of the coil to frozen globule transition in heteropolymers

Pande, V. S., Grosberg, A. Y., & Tanaka, T. (1997) · The Journal of Chemical Physics · doi:10.1063/1.474875 · Cited by 29 · see citing works

[The theory of cooperative transitions in protein globules].

Shakhnovich, E. I., & Finkel'shteĭn (1982) · PubMed · Cited by 28 · see citing works

Steric Constraints in Model Proteins

Micheletti, C., Banavar, J. R., Maritan, A., et al. (1998) · Physical Review Letters · doi:10.1103/physrevlett.80.5683 · Cited by 26 · see citing works

Design of copolymeric materials

Kurosky, T., & Deutsch, J. M. (1995) · Journal of Physics A Mathematical and General · doi:10.1088/0305-4470/28/14/003 · Cited by 26 · see citing works

Investigation of protein unfolding and stability by computer simulation

van Gunsteren, W. F., Hünenberger, P. H., Kovacs, H., et al. (1995) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.1995.0045 · Cited by 25 · see citing works

Thinking combinatorially

Kauffman, S. A., & Ellington, A. D. (1999) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(99)80040-4 · Cited by 19 · see citing works

Freezing of compact random heteropolymers with correlated sequence fluctuations

Chakraborty, A. K., Shakhnovich, E. I., & Pande, V. S. (1998) · The Journal of Chemical Physics · doi:10.1063/1.475539 · Cited by 16 · see citing works

Reversible molecular adsorption as a tool to observe freezing and to perform design of heteropolymer gels

Tanaka, T., Enoki, T., Grosberg, A. Y., Masamune, S., Oya, T., Takaoka, Y., Tanaka, K., Wang, C., & Wang, G. (1998) · Berichte der Bunsengesellschaft für physikalische Chemie · doi:10.1002/bbpc.19981021103 · Cited by 16 · see citing works

Models of protein interactions: how to choose one

Du, R., Grosberg, A. Y., & Tanaka, T. (1998) · Folding and Design · doi:10.1016/s1359-0278(98)00028-5 · Cited by 13 · see citing works

ON THE MEAN FIELD THEORY OF RANDOM HETEROPOLYMERS

Franz, S., Mézard, M., & Parisi, G. (1992) · International Journal of Neural Systems · doi:10.1142/s0129065792000528 · Cited by 11 · see citing works

On the properties of polymer globules in the high density limit

Witelski, T. P., Grosberg, A. Y., & Tanaka, T. (1998) · The Journal of Chemical Physics · doi:10.1063/1.476361 · Cited by 11 · see citing works

The coil–globule transition of polymers of long rigid monomers connected by flexible spacers

Sear, R. P. (1997) · The Journal of Chemical Physics · doi:10.1063/1.474987 · Cited by 8 · see citing works

Analyticity of the partition function of the random energy model

Koukiou, F. (1993) · Journal of Physics A Mathematical and General · doi:10.1088/0305-4470/26/23/003 · Cited by 7 · see citing works

[A theory of heteropolymers with frozen random primary structure: properties of the globular state, coil-globule transitions and possible biophysical applications].

Grosberg, A. Y., & Shakhnovich, E. I. (1987) · PubMed · Cited by 3 · see citing works

Random Samples

Holden, C. (1995) · Science · doi:10.1126/science.269.5231.1675 · Cited by 3 · see citing works

Overlap properties and adsorption transition of two Hamiltonian paths

Franz, S., Garel, T., & Orland, H. (1999) · The European Physical Journal B · doi:10.1007/s100510050957 · Cited by 2 · see citing works

Finding low-energy conformations of lattice protein models by quantum annealing

Perdomo-Ortiz, A., Dickson, N., Drew-Brook, M., Rose, G., & Aspuru-Guzik, A. (2012) · Scientific Reports · doi:10.1038/srep00571 · Cited by 366 · see citing works

Simulating Chemistry Using Quantum Computers

Kassal, I., Whitfield, J. D., Perdomo-Ortiz, A., Yung, M.-H., & Aspuru-Guzik, A. (2011) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-032210-103512 · Cited by 352 · see citing works

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

Li, W., Wolynes, P. G., & Takada, S. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1018983108 · Cited by 159 · see citing works

Construction of Energy Functions for Lattice Heteropolymer Models: Efficient Encodings for Constraint Satisfaction Programming and Quantum Annealing

Babbush, R., Perdomo‐Ortiz, A., O'Gorman, B., Macready, W., & Aspuru‐Guzik, A. (2014) · Advances in Chemical Physics · doi:10.1002/9781118755815.ch05 · Cited by 45 · see citing works

Lethal mutants and truncated selection together solve a paradox of the origin of life

Saakian, D. B., Biebricher, C. K., & Hu, C.-K. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021904 · Cited by 27 · see citing works

Reshaping the Protein Folding Pathway by Osmolyte via its Effects on the Folding Intermediates

Sharma, G., Dar, T., & Singh, L. (2015) · Current Protein &amp; Peptide Science · doi:10.2174/1389203716666150623104330 · Cited by 10 · see citing works

Comparing the Folding and Misfolding Energy Landscapes of Phosphoglycerate Kinase

Agócs, G., Szabó, B. T., Köhler, G., et al. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.05.006 · Cited by 7 · see citing works

Biosynthetic Protein Folding and Molecular Chaperons

Fedorov, A. N. (2022) · Biochemistry (Moscow) · doi:10.1134/s0006297922140115 · Cited by 5 · see citing works

Improving folding properties of computationally designed proteins

Bjerre, B., Nissen, J. N., Madsen, M. G., Fahrig‐Kamarauskaitė, J., Norrild, R. K., Holm, P. C., Nordentoft, M. K., O’Shea, C., Willemoës, M., Johansson, K. E., et al. (2019) · Protein Engineering Design and Selection · doi:10.1093/protein/gzz025 · Cited by 5 · see citing works

Using Single-Molecule Chemo-Mechanical Unfolding to Simultaneously Probe Multiple Structural Parameters in Protein Folding

Guinn, E. J., & Marqusee, S. (2019) · Methods and Protocols · doi:10.3390/mps2020032