The Protein Folding Problem

A peptidomimetic siRNA transfection reagent for highly effective gene silencing

Konca, Y. U., Dehan, E., Ouerfelli, O., Piano, F., Zuckermann, R. N., Pagano, M., & Kirshenbaum, K. (2006) · Molecular BioSystems · doi:10.1039/b603229j · Cited by 63

Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding.

White, G. W., Gianni, S., Grossmann, J., Jemth, P., Fersht, A., & Daggett, V. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.05.005 · Cited by 61

The topomer-sampling model of protein folding

Debe, D. A., Carlson, M. J., & Goddard, W. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.6.2596 · Cited by 60

Nanosecond Folding Dynamics of a Three-Stranded β-Sheet

Xu, Y., Purkayastha, P., & Gai, F. (2006) · Journal of the American Chemical Society · doi:10.1021/ja064865+ · Cited by 58

Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding Intermediate Ensemble

Sridevi, K., Lakshmikanth, G. S., Krishnamoorthy, G., & Udgaonkar, J. B. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.12.083 · Cited by 58

Kinetically Controlled Folding of the Serpin Plasminogen Activator Inhibitor 1

Wang, Z., Mottonen, J. M., & Goldsmith, E. J. (1996) · Biochemistry · doi:10.1021/bi961214p · Cited by 58

Role of backbone solvation in determining thermodynamic β propensities of the amino acids

Avbelj, F., & Baldwin, R. L. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032665499 · Cited by 58

Folding Kinetics of Two-state Proteins: Effect of Circularization, Permutation, and Crosslinks

Weikl, T. R., & Dill, K. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00884-2 · Cited by 57

The Protein Folding Transition State: What Are φ-Values Really Telling Us?

Raleigh, D. P., & Plaxco, K. W. (2005) · Protein and Peptide Letters · doi:10.2174/0929866053005809 · Cited by 54

Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water

Elmer, S. P., Park, S., & Pande, V. S. (2005) · The Journal of Chemical Physics · doi:10.1063/1.2001648 · Cited by 54

The Notch Ankyrin Domain Folds via a Discrete, Centralized Pathway

Bradley, C. M., & Barrick, D. (2006) · Structure · doi:10.1016/j.str.2006.06.013 · Cited by 53

Analysis of 'downhill' protein folding

Ferguson, N. S., Sharpe, T., Johnson, C. M., Schartau, P. J., & Fersht, A. R. (2007) · Nature · doi:10.1038/nature05643 · Cited by 52

Reducing the computational complexity of protein folding via fragment folding and assembly

Haspel, N., Tsai, C., Wolfson, H. J., & Nussinov, R. (2003) · Protein Science · doi:10.1110/ps.0232903 · Cited by 52

Conformational entropic barriers in topology-dependent protein folding: perspectives from a simple native-centric polymer model

Wallin, S., & Chan, H. S. (2006) · Journal of Physics Condensed Matter · doi:10.1088/0953-8984/18/14/s14 · Cited by 51

Secondary structure length as a determinant of folding rate of proteins with two‐ and three‐state kinetics

Huang, J. T., Cheng, J., & Chen, H. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21282 · Cited by 47

The slow folding reaction of barstar: the core tryptophan region attains tight packing before substantial secondary and tertiary structure formation and final compaction of the polypeptide chain 1 1Edited by C. R. Matthews

Sridevi, K., Juneja, J., Bhuyan, A. K., Krishnamoorthy, G., & Udgaonkar, J. B. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4060 · Cited by 46

Ab Initio Folding of Albumin Binding Domain from All-Atom Molecular Dynamics Simulation

Lei, H., & Duan, Y. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp0704867 · Cited by 40

Exploring subdomain cooperativity in T4 lysozyme II: Uncovering the C‐terminal subdomain as a hidden intermediate in the kinetic folding pathway

Cellitti, J. F., Bernstein, R., & Marqusee, S. (2007) · Protein Science · doi:10.1110/ps.062632807 · Cited by 40

Structural genomics: keeping up with expanding knowledge of the protein universe

Grabowski, M., Joachimiak, A., Otwinowski, Z., & Minor, W. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.06.003 · Cited by 40

Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates

Snow, C. D., Rhee, Y. M., & Pande, V. S. (2006) · Biophysical Journal · doi:10.1529/biophysj.105.075689 · Cited by 39

Brownian dynamics simulation of protein folding: A study of the diffusion‐collision model

Lee, S., Karplus, M., Bashford, D., & Weaver, D. L. (1987) · Biopolymers · doi:10.1002/bip.360260404 · Cited by 38

Class‐specific correlations between protein folding rate, structure‐derived, and sequence‐derived descriptors

Kuznetsov, I. B., & Rackovsky, S. R. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10518 · Cited by 36

Transition-states in protein folding kinetics: the structural interpretation of Phi values.

Weikl, T., & Dill, K. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.10.082 · Cited by 35

Direct folding simulation of α‐helices and β‐hairpins based on a single all‐atom force field with an implicit solvation model

Jang, S., Kim, E., & Pak, Y. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21173 · Cited by 35

Predicting coupling limits from an experimentally determined energy landscape

Street, T. O., Bradley, C. M., & Barrick, D. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608756104 · Cited by 34

Routes are trees: The parsing perspective on protein folding

Hockenmaier, J., Joshi, A. K., & Dill, K. A. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21195 · Cited by 33

Foldamer dynamics expressed via Markov state models. II. State space decomposition

Elmer, S. P., Park, S., & Pande, V. S. (2005) · The Journal of Chemical Physics · doi:10.1063/1.2008230 · Cited by 32

Calculation of Mutational Free Energy Changes in Transition States for Protein Folding

Lindorff‐Larsen, K., Paci, E., Serrano, L. G., Dobson, C. M., & Vendruscolo, M. (2003) · Biophysical Journal · doi:10.1016/s0006-3495(03)74556-1 · Cited by 32

Exploring zipping and assembly as a protein folding principle

Voelz, V. A., & Dill, K. A. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21234 · Cited by 31

Fluctuations of primary ubiquitin folding intermediates in a force clamp

Gräter, F., & Grubmüller, H. (2006) · Journal of Structural Biology · doi:10.1016/j.jsb.2006.11.005 · Cited by 31

Low barrier kinetics: Dependence on observables and free energy surface

Ma, H., & Gruebele, M. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20311 · Cited by 31

Folding Time Distributions as an Approach to Protein Folding Kinetics

Chekmarev, S. F., Krivov, S. V., & Karplus, M. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp047012h · Cited by 30

Probe‐dependent and nonexponential relaxation kinetics: Unreliable signatures of downhill protein folding

Hagen, S. J. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21342 · Cited by 29

Role of unfolded state heterogeneity and en‐route ruggedness in protein folding kinetics

Ellison, P. A., & Cavagnero, S. (2006) · Protein Science · doi:10.1110/ps.051758206 · Cited by 28

The Transition State for Folding of a Peripheral Subunit-binding Domain Contains Robust and Ionic-strength Dependent Characteristics

Ferguson, N. S., Sharpe, T., Johnson, C. M., & Fersht, A. R. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.12.016 · Cited by 27

Structural Examination of Φ-Value Analysis in Protein Folding

Feng, H., Vu, N., Zhou, Z., & Bai, Y. (2004) · Biochemistry · doi:10.1021/bi048126m · Cited by 27

Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding

Meisner, W. K., & Sosnick, T. R. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404895101 · Cited by 27

Hierarchical folding of cytochrome c

Yeh, S., & Rousseau, D. L. (2000) · Nature Structural Biology · doi:10.1038/75831 · Cited by 25

Folding mechanism of Pseudomonas aeruginosa cytochrome c 551 : role of electrostatic interactions on the hydrophobic collapse and transition state properties 1 1Edited by P. E. Wright

Travaglini‐Allocatelli, C., Cutruzzolà, F., Bigotti, M. G., Staniforth, R. A., & Brunori, M. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2852 · Cited by 25

Experimental Investigation of the Frequency and Substitution Dependence of Negative φ-Values in Two-State Proteins

Rios, M. A. D. L., Daneshi, M., & Plaxco, K. W. (2005) · Biochemistry · doi:10.1021/bi0505621 · Cited by 24

Alteration of the disulfide‐coupled folding pathway of BPTI by circular permutation

Bulaj, G. W., Koehn, R. E., & Goldenberg, D. P. (2004) · Protein Science · doi:10.1110/ps.03563704 · Cited by 22

Scaling of Folding Properties in Go Models of Proteins

Cieplak, M., & Hoàng, T. X. (2000) · Journal of Biological Physics · doi:10.1023/a:1010359024559 · Cited by 18

Modulation of the Folding Energy Landscape of Cytochrome c with Salt

Zhong, S., Rousseau, D. L., & Yeh, S. (2004) · Journal of the American Chemical Society · doi:10.1021/ja0459431 · Cited by 18

Loop‐closure events during protein folding: Rationalizing the shape of Φ‐value distributions

Weikl, T. R. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20504 · Cited by 17

Substructural cooperativity and parallel versus sequential events during protein unfolding

Reich, L. “., & Weikl, T. R. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20966 · Cited by 17

Search for folding nuclei in native protein structures

Shmygelska, A. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti1050 · Cited by 16

Combinatorial Approaches to Probe the Sequence Determinants of Protein Aggregation and Amyloidogenicity

Wurth, C., Kim, W., & Hecht, M. H. (2006) · Protein and Peptide Letters · doi:10.2174/092986606775338506 · Cited by 15

Statistical Mechanics of Helix Bundles Using a Dynamic Programming Approach

Lucas, A. R., Huang, L., Joshi, A. K., & Dill, K. A. (2007) · Journal of the American Chemical Society · doi:10.1021/ja067153s · Cited by 14

Computational linguistics: A new tool for exploring biopolymer structures and statistical mechanics

Dill, K. A., Lucas, A. R., Hockenmaier, J., Huang, L., Chiang, D., & Joshi, A. K. (2007) · Polymer · doi:10.1016/j.polymer.2007.05.018 · Cited by 14

Highly accurate protein structure prediction with AlphaFold

Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764

Improved protein structure prediction using potentials from deep learning

Senior, A. W., Evans, R., Jumper, J., Kirkpatrick, J., Sifre, L., Green, T., Qin, C., Žídek, A., Nelson, A. W. R., Bridgland, A., et al. (2020) · Nature · doi:10.1038/s41586-019-1923-7 · Cited by 3,378

The Protein-Folding Problem, 50 Years On

Dill, K. A., & MacCallum, J. L. (2012) · Science · doi:10.1126/science.1219021 · Cited by 1,699

Biological and Chemical Approaches to Diseases of Proteostasis Deficiency

Powers, E. T., Morimoto, R. I., Dillin, A., Kelly, J. W., & Balch, W. E. (2009) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.052308.114844 · Cited by 1,149

Multiblock Polymers: Panacea or Pandora’s Box?

Bates, F. S., Hillmyer, M. A., Lodge, T. P., Bates, C. M., Delaney, K. T., & Fredrickson, G. H. (2012) · Science · doi:10.1126/science.1215368 · Cited by 1,147

The protein folding problem: when will it be solved?

Dill, K. A., Ozkan, S. B., Weikl, T. R., Chodera, J. D., & Voelz, V. A. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.06.001 · Cited by 261

The Protein-Folding Problem, 50 Years On

Dill, K. A., & MacCallum, J. L. (2012) · Science · doi:10.1126/science.1219021 · Cited by 1,699

Multiple Minima Problem in Protein Folding: αBB Global Optimization Approach

Klepeis, J. L., & Floudas, C. A. (2001) · Encyclopedia of Optimization · doi:10.1007/0-306-48332-7_325 · Cited by 1

Protein structure prediction and design

Morea, V., Leplae, R., & Tramontano, A. L. (1998) · Biotechnology annual review · doi:10.1016/s1387-2656(08)70070-x · Cited by 9

Protein folding prediction

Ma, B. (2016) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/n972016-00658 · Cited by 1