Elucidating the folding problem of helical peptides using empirical parameters

NMR with Proteins and Nucleic Acids

Wüthrich, K. (1986) · Europhysics news · doi:10.1051/epn/19861701011 · Cited by 8,028

Statistical mechanics of chain molecules

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

NMR of Proteins and Nucleic Acids

(2006) · Royal Society of Chemistry eBooks · doi:10.1039/9781847555236-00336 · Cited by 5,874

Determination of the helix and β form of proteins in aqueous solution by circular dichroism

Chen, Y.-H., Yang, J. T., & Chau, K. H. (1974) · Biochemistry · doi:10.1021/bi00713a027 · Cited by 2,070

Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains

Zimm, B., & Bragg, J. K. (1959) · The Journal of Chemical Physics · doi:10.1063/1.1730390 · Cited by 1,801

Structure of ubiquitin refined at 1.8 A resolution.

Vijay-Kumar, S., Bugg, C., & Cook, W. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90679-6 · Cited by 1,636

Amino Acid Preferences for Specific Locations at the Ends of α Helices

Richardson, J. S., & Richardson, D. C. (1988) · Science · doi:10.1126/science.3381086 · Cited by 1,364

A Thermodynamic Scale for the Helix-Forming Tendencies of the Commonly Occurring Amino Acids

O’Neil, K. T., & DeGrado, W. F. (1990) · Science · doi:10.1126/science.2237415 · Cited by 1,186

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 1,068

A Novel, Highly Stable Fold of the Immunoglobulin Binding Domain of Streptococcal Protein G

Gronenborn, A. M., Filpula, D. R., Essig, N. Z., Achari, A., Whitlow, M. D., Wingfield, P. T., & Clore, G. M. (1991) · Science · doi:10.1126/science.1871600 · Cited by 816

Interactions with Aromatic Rings in Chemical and Biological Recognition

Meyer, E. A., Castellano, R. K., & Diederich, F. (2003) · Angewandte Chemie International Edition · doi:10.1002/anie.200390319 · Cited by 3,554

A Helix Propensity Scale Based on Experimental Studies of Peptides and Proteins

Pace, C. N., & Scholtz, J. M. (1998) · Biophysical Journal · doi:10.1016/s0006-3495(98)77529-0 · Cited by 1,074

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

Best, R., & Hummer, G. (2009) · Journal of Physical Chemistry B · doi:10.1021/jp901540t · Cited by 826

Trifluoroethanol and colleagues: cosolvents come of age. Recent studies with peptides and proteins

Buck, M. (1998) · Quarterly Reviews of Biophysics · doi:10.1017/s003358359800345x · Cited by 829

A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design

Beno, B. R., Yeung, K., Bartberger, M. D., Pennington, L. D., & Meanwell, N. A. (2015) · Journal of Medicinal Chemistry · doi:10.1021/jm501853m · Cited by 791

Sensitivity of secondary structure propensities to sequence differences between α‐ and γ‐synuclein: Implications for fibrillation

Marsh, J. A., Singh, V. K., Jia, Z., & Forman-Kay, J. D. (2006) · Protein Science · doi:10.1110/ps.062465306 · Cited by 730

Design of Folded Peptides

Venkatraman, J., Shankaramma, S. C., & Balaram, P. (2001) · Chemical Reviews · doi:10.1021/cr000053z · Cited by 699

FIZZ1, a novel cysteine‐rich secreted protein associated with pulmonary inflammation, defines a new gene family

Holcomb, I. N., Kabakoff, R. C., Chan, B., Baker, T. W., Gurney, A. L., Henzel, W. J., Nelson, C., Lowman, H. B., Wright, B. D., Skelton, N. J., et al. (2000) · The EMBO Journal · doi:10.1093/emboj/19.15.4046 · Cited by 662

A simple model for calculating the kinetics of protein folding from three-dimensional structures

Muñoz, V., & Eaton, W. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.20.11311 · Cited by 627

De Novo Design and Structural Characterization of Proteins and Metalloproteins

DeGrado, W. F., Summa, C. M., Pavone, V., Nastri, F., & Lombardi, A. (1999) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.68.1.779 · Cited by 572

Wechselwirkungen mit aromatischen Ringen in chemischen und biologischen Erkennungsprozessen

Meyer, E. A., Castellano, R. K., & Diederich, F. (2003) · Angewandte Chemie · doi:10.1002/ange.200390290 · Cited by 552

Is protein folding hierarchic? I. Local structure and peptide folding

Baldwin, R. L., & Rose, G. D. (1999) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(98)01346-2 · Cited by 492

Fast Kinetics and Mechanisms in Protein Folding

Eaton, W. A., Muñoz, V., Hagen, S. J., Jas, G. S., Lapidus, L. J., Henry, E. R., & Hofrichter, J. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.327 · Cited by 489

Are Current Molecular Dynamics Force Fields too Helical?

Best, R. B., Buchete, N., & Hummer, G. (2008) · Biophysical Journal · doi:10.1529/biophysj.108.132696 · Cited by 452

α-Helical stabilization by side chain shielding of backbone hydrogen bonds

Garcı́a, A. E., & Sanbonmatsu, K. Y. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.042496899 · Cited by 442

Elucidating the folding problem of α-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters 1 1Edited by A. R. Fersht

Lacroix, E., Viguera, A. R., & Serrano, L. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2145 · Cited by 439

Salt bridges: Geometrically specific, designable interactions

Donald, J. E., Kulp, D. W., & DeGrado, W. F. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22927 · Cited by 404

A Comparative Study of the Relationship Between Protein Structure and β-Aggregation in Globular and Intrinsically Disordered Proteins

Linding, R., Schymkowitz, J. W. H., Rousseau, F., Diella, F., & Serrano, L. G. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.06.088 · Cited by 386

Local Structural Elements in the Mostly Unstructured Transcriptional Activation Domain of Human p53

Lee, H., Mok, K. H., Muhandiram, R., Park, K.-H., Suk, J.-E., Kim, D., Chang, J., Sung, Y. C., Choi, K. Y., & Han, K. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m003107200 · Cited by 329

N‐ and C‐capping preferences for all 20 amino acids in α‐helical peptides

Doig, A. J., & Baldwin, R. L. (1995) · Protein Science · doi:10.1002/pro.5560040708 · Cited by 319

Protein Design: From the Aspect of Water Solubility and Stability

Qing, R., Hao, S., Smorodina, E., Jin, D., Zalevsky, A. O., & Zhang, S. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00757 · Cited by 334

Hydrogen bonding stabilizes globular proteins

Myers, J. K., & Pace, C. N. (1996) · Biophysical Journal · doi:10.1016/s0006-3495(96)79401-8 · Cited by 308

Energetics of Protein Folding

Baldwin, R. L. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.05.078 · Cited by 312

Intrinsic secondary structure propensities of the amino acids, using statistical ϕ–ψ matrices: Comparison with experimental scales

Muñoz, V., & Serrano, L. G. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340200403 · Cited by 295

A Highly Amyloidogenic Region of Hen Lysozyme

Frare, E., de Laureto, P. P., Zurdo, J., Dobson, C. M., & Fontana, A. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.05.056 · Cited by 285

De novo design and structural analysis of a model β-hairpin peptide system

Ramírez-Alvarado, M., Blanco, F. J., & Serrano, L. G. (1996) · Nature Structural Biology · doi:10.1038/nsb0796-604 · Cited by 280

Ionic polypeptides with unusual helical stability

Lu, H., Wang, J., Bai, Y., Lang, J. W., Liu, S., Lin, Y., & Cheng, J. (2011) · Nature Communications · doi:10.1038/ncomms1209 · Cited by 272

Mechanism for the α‐helix to β‐hairpin transition

Ding, F., Borreguero, J. M., Buldyrey, S. V., Stanley, E., & Dokholyan, N. V. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10468 · Cited by 272

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse

Best, R. B., & Mittal, J. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp108618d · Cited by 261

Conformational propensities of intrinsically disordered proteins influence the mechanism of binding and folding

Arai, M., Sugase, K., Dyson, H. J., & Wright, P. E. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1512799112 · Cited by 250

Helix propagation and N‐cap propensities of the amino acids measured in alanine‐based peptides in 40 volume percent trifluoroethanol

Rohl, C. A., Chakrabartty, A., & Baldwin, R. L. (1996) · Protein Science · doi:10.1002/pro.5560051225 · Cited by 256

Im7 folding mechanism: misfolding on a path to the native state

Capaldi, A. P., Kleanthous, C., & Radford, S. E. (2002) · Nature Structural Biology · doi:10.1038/nsb757 · Cited by 249

Short amino acid stretches can mediate amyloid formation in globular proteins: The Src homology 3 (SH3) case

Ventura, S., Zurdo, J., Narayanan, S., Parreño, M., Mangues, R., Reif, B., Chiti, F., Giannoni, E., Dobson, C. M., Avilés, F. X., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308249101 · Cited by 244

Elucidating the Folding Problem of Helical Peptides using Empirical Parameters. III>Temperature and pH Dependence

Muñoz, V., & Serrano, L. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.0024 · Cited by 251

Temperature‐dependent structural changes in intrinsically disordered proteins: Formation of α‒helices or loss of polyproline II?

Kjærgaard, M., Nørholm, A., Hendus-Altenburger, R., Pedersen, S. F., Poulsen, F. M., & Kragelund, B. B. (2010) · Protein Science · doi:10.1002/pro.435 · Cited by 238

Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures

Swindells, M. B., MacArthur, M. W., & Thornton, J. M. (1995) · Nature Structural Biology · doi:10.1038/nsb0795-596 · Cited by 236

The interrelationships of side-chain and main-chain conformations in proteins

Chakrabarti, P., & Pal, D. (2001) · Progress in Biophysics and Molecular Biology · doi:10.1016/s0079-6107(01)00005-0 · Cited by 224

The hydrophobic effect in protein folding

Lins, L., & Brasseur, R. (1995) · The FASEB Journal · doi:10.1096/fasebj.9.7.7737462 · Cited by 224

A physical basis for protein secondary structure

Srinivasan, R., & Rose, G. D. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.25.14258 · Cited by 207

Structured disorder and conformational selection

Tsai, C., Ma, B., Sham, Y. Y., Kumar, S., & Nussinov, R. (2001) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.1107 · Cited by 202

Rationally improving LOV domain–based photoswitches

Strickland, D., Yao, X., Gawlak, G., Rosen, M. K., Gardner, K. H., & Sosnick, T. R. (2010) · Nature Methods · doi:10.1038/nmeth.1473 · Cited by 201

How fast is protein hydrophobic collapse?

Sadqi, M., Lapidus, L. J., & Muñoz, V. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2033863100 · Cited by 198

A transcription-factor-binding surface of coactivator p300 is required for haematopoiesis

Kasper, L. H., Boussouar, F., Ney, P. A., Jackson, C. W., Rehg, J. E., van Deursen, J. M., & Brindle, P. K. (2002) · Nature · doi:10.1038/nature01062 · Cited by 193

Aromatic interactions in peptides: Impact on structure and function

Waters, M. L. (2004) · Biopolymers · doi:10.1002/bip.20144 · Cited by 186

Folding amphipathic helices into membranes: amphiphilicity trumps hydrophobicity.

Fernández-Vidal, M., Jayasinghe, S. A., Ladokhin, A., & White, S. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.05.016 · Cited by 173

α‐Helix formation: Discontinuous molecular dynamics on an intermediate‐resolution protein model

Smith, A. V., & Hall, C. K. (2001) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.1100 · Cited by 185

Reactive and Bioactive Cationic α‐Helical Polypeptide Template for Nonviral Gene Delivery

Gabrielson, N. P., Lu, H., Yin, L., Li, D., Wang, F., & Cheng, J. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.201104262 · Cited by 180

Injectable tissue integrating networks from recombinant polypeptides with tunable order

Roberts, S., Harmon, T. S., Schaal, J. L., Miao, V. N., Li, K., Hunt, A. C., Wen, Y., Oas, T. G., Collier, J. H., Pappu, R. V., et al. (2018) · Nature Materials · doi:10.1038/s41563-018-0182-6 · Cited by 179

New insights into the determination of HDL structure by apolipoproteins

Phillips, M. C. (2012) · Journal of Lipid Research · doi:10.1194/jlr.r034025 · Cited by 172

Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements.

Blanco, F. J., & Serrano, L. (1995) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1995.0634h.x · Cited by 148

An autonomous folding unit mediates the assembly of two-stranded coiled coils

Kammerer, R. A., Schulthess, T., Landwehr, R., Lustig, A., Engel, J., Aebi, U., & Steinmetz, M. O. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.23.13419 · Cited by 174

Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine

Winn, P. J., Lüdemann, S. K., Gauges, R., Lounnas, V., & Wade, R. C. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.082522999 · Cited by 173

The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation

Shimada, J., & Shakhnovich, E. I. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.162268099 · Cited by 172

Solution NMR studies of amphibian antimicrobial peptides: linking structure to function?

Haney, E. F., Hunter, H., Matsuzaki, K., & Vogel, H. (2009) · Biochimica et Biophysica Acta · doi:10.1016/j.bbamem.2009.01.002 · Cited by 166

Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain

Villegas, S., Martínez, J. C., Avilés, F. X., & Serrano, L. G. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2158 · Cited by 168

Dissecting the stability of a β-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the β-turn and β-strand contributions to folding 1 1Edited by P. E. Wright

Griffiths‐Jones, S., Maynard, A. J., & Searle, M. S. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3119 · Cited by 163

Helical Propensity in an Intrinsically Disordered Protein Accelerates Ligand Binding

Iešmantavičius, V., Dogan, J., Jemth, P., Teilum, K., & Kjærgaard, M. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201307712 · Cited by 162

Identification of Specific DNA Binding Residues in the TCP Family of Transcription Factors in Arabidopsis

Aggarwal, P., Gupta, M. D., Joseph, A. P., Chatterjee, N., Srinivasan, N., & Nath, U. (2010) · The Plant Cell · doi:10.1105/tpc.109.066647 · Cited by 157

Sequence space, folding and protein design

Cordes, M. H. J., Davidson, A. R., & Sauer, R. T. (1996) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(96)80088-1 · Cited by 154

Matching theory and experiment in protein folding

Alm, E. J., & Baker, D. A. (1999) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(99)80027-x · Cited by 157

WW: An isolated three‐stranded antiparallel β‐sheet domain that unfolds and refolds reversibly; evidence for a structured hydrophobic cluster in urea and GdnHCl and a disordered thermal unfolded state

Koepf, E. K., Petrassi, H. M., Sudol, M., & Kelly, J. W. (1999) · Protein Science · doi:10.1110/ps.8.4.841 · Cited by 151

Helical structure and stability in human apolipoprotein A-I by hydrogen exchange and mass spectrometry

Chetty, P. S., Mayne, L. C., Lund‐Katz, S., Stranz, D. D., Englander, S. W., & Phillips, M. C. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909708106 · Cited by 150

Formation and stability of β-hairpin structures in polypeptides

Blanco, F. J., Ramı́rez-Alvarado, M., & Serrano, L. G. (1998) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(98)80017-1 · Cited by 150

EPI-001, A Compound Active against Castration-Resistant Prostate Cancer, Targets Transactivation Unit 5 of the Androgen Receptor

Mol, E. D., Fenwick, R. B., Phang, C. T. W., Buzón, V., Szulc, E., de la Fuente, A., Escobedo, A., García, J., Bertoncini, C. W., Estébanez‐Perpiñá, E., et al. (2016) · ACS Chemical Biology · doi:10.1021/acschembio.6b00182 · Cited by 148

The folding thermodynamics and kinetics of crambin using an all-atom monte carlo simulation11Edited by A. R. Fersht

Shimada, J., Kussell, E. L., & Shakhnovich, E. I. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4586 · Cited by 144

Computational Design and Characterization of a Monomeric Helical Dinuclear Metalloprotein

Calhoun, J. R., Kono, H., Lahr, S. J., Wang, W., DeGrado, W. F., & Saven, J. G. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.10.004 · Cited by 144

Atomistic folding simulations of the five helix bundle protein λ6–85

Bowman, G., Voelz, V. A., & Pande, V. (2011) · Journal of the American Chemical Society · doi:10.1021/ja106936n · Cited by 139

Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α-Helix and β-Hairpin Formation

Best, R. B., Mittal, J., Feig, M., & MacKerell, A. D. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.07.042 · Cited by 136

Helices and Sheets in vacuo

Jarrold, M. F. (2007) · Physical Chemistry Chemical Physics · doi:10.1039/b612615d · Cited by 136

De novo design of a monomeric three‐stranded antiparallel β‐sheet

de Alba, E., Santoro, J., Rico, M., & Jiménez, M. A. (1999) · Protein Science · doi:10.1110/ps.8.4.854 · Cited by 136

[1] Deciphering rules of helix stability in peptides

Rohl, C. A., & Baldwin, R. L. (1998) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(98)95032-7 · Cited by 128

Structural Characterization of the LEM Motif Common to Three Human Inner Nuclear Membrane Proteins

Laguri, C., Gilquin, B., Wolff, N., Lebrun, R., Courchay, K., Callebaut, I., Worman, H. J., & Zinn‐Justin, S. (2001) · Structure · doi:10.1016/s0969-2126(01)00611-6 · Cited by 125

Lysine Residues Direct the Chlorination of Tyrosines in YXXK Motifs of Apolipoprotein A-I When Hypochlorous Acid Oxidizes High Density Lipoprotein

Bergt, C., Fu, X., Saifee, N. H., Kao, J. L.-F., & Heinecke, J. W. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309046200 · Cited by 123

Contributions of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure in λ repressor

Marqusee, S., & Sauer, R. T. (1994) · Protein Science · doi:10.1002/pro.5560031207 · Cited by 122

The hydrophobic-staple motif and a role for loop-residues in α-helix stability and protein folding

Muñoz, V., Blanco, F., & Serrano, L. (1995) · Nature Structural Biology · doi:10.1038/nsb0595-380 · Cited by 118

Characterization of the Structure and the Amyloidogenic Properties of the Josephin Domain of the Polyglutamine-containing Protein Ataxin-3

Masino, L., Nicastro, G., Menon, R. P., Piaz, F. D., Calder, L. J., & Pastore, A. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.09.065 · Cited by 119

Human ACE2 peptide-mimics block SARS-CoV-2 pulmonary cells infection

Karoyan, P., Vieillard, V., Gómez‐Morales, L., Odile, E., Guihot, A., Luyt, C. E., Denis, A., Grondin, P., & Lequin, O. (2021) · Communications Biology · doi:10.1038/s42003-021-01736-8 · Cited by 120

A synthetic peptide adhesion epitope as a novel antimicrobial agent

Kelly, C. G., Younson, J., Hikmat, B., Todryk, S., Czisch, M., Haris, P., Flindall, I., Newby, C. S., Mallet, A., Ma, J., et al. (1999) · Nature Biotechnology · doi:10.1038/5213 · Cited by 113

Mechanisms of Fast Protein Folding

Myers, J. K., & Oas, T. G. (2002) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.71.110601.135346 · Cited by 115

Computational design of water-soluble analogues of the potassium channel KcsA

Slovic, A. M., Kono, H., Lear, J. D., Saven, J. G., & DeGrado, W. F. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0306417101 · Cited by 114

Coupled Folding and Binding of the Disordered Protein PUMA Does Not Require Particular Residual Structure

Rogers, J. M., Wong, C. T., & Clarke, J. (2014) · Journal of the American Chemical Society · doi:10.1021/ja4125065 · Cited by 113

Rational design of aggregation-resistant bioactive peptides: Reengineering human calcitonin

Fowler, S. A., Poon, S., Muff, R., Chiti, F., Dobson, C. M., & Zurdo, J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0501215102 · Cited by 114

Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides

Schneider, G., Sjöling, S., Wallin, E. J., Wrede, P., Glaser, E. G., & von HEIJNE, G. (1998) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19980101)30:1 · Cited by 112

Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes

Matthes, D., & de Groot, B. L. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2009.04.061 · Cited by 111

Synergy between simulation and experiment in describing the energy landscape of protein folding

Ladurner, A. G., Itzhaki, L. S., Daggett, V., & Fersht, A. R. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.15.8473 · Cited by 111

Intrinsically Disordered Energy Landscapes

Chebaro, Y., Ballard, A. J., Chakraborty, D., & Wales, D. J. (2015) · Scientific Reports · doi:10.1038/srep10386 · Cited by 110

Modeling the paramyxovirus hemagglutinin-neuraminidase protein

Epa, V. C. (1997) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(199711)29:3 · Cited by 14

α-Helix formation by peptides of defined sequence

Baldwin, R. L. (1995) · Biophysical Chemistry · doi:10.1016/0301-4622(94)00146-b · Cited by 109

Conformational Properties of Four Peptides Spanning the Sequence of Hen Lysozyme

Yang, J. J., Buck, M., Pitkeathly, M. C., Kotik, M., Haynie, D. T., Dobson, C. M., & Radford, S. E. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0513 · Cited by 109

Interaction between water and polar groups of the helix backbone: An important determinant of helix propensities

Luo, P., & Baldwin, R. L. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.9.4930 · Cited by 108

Recent advances in helix–coil theory

Doig, A. J. (2002) · Biophysical Chemistry · doi:10.1016/s0301-4622(02)00170-9 · Cited by 106

Stabilization of MyoD by Direct Binding to p57Kip2

Reynaud, E. G., Leibovitch, M.-P., Tintignac, L. A. J., Pelpel, K., Guillier, M., & Leibovitch, S. A. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m907412199 · Cited by 104

Molecular Recognition of Paxillin LD Motifs by the Focal Adhesion Targeting Domain

Hoellerer, M. K., Noble, M. E. M., Labesse, G., Campbell, I. D., Werner, J. M., & Arold, S. T. (2003) · Structure · doi:10.1016/j.str.2003.08.010 · Cited by 107

The Tryptophan/Histidine interaction in α-helices

Fernández-Recio, J., Vazquez, A., Civera, C., Sevilla, P., & Sancho, J. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0831 · Cited by 77

Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble

Shoemaker, B. A., Wang, J., & Wolynes, P. G. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2613 · Cited by 104

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