PMID: 
Reviews - 1enh mentioned but not cited (4)
- Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. Schnieders MJ, Baker NA, Ren P, Ponder JW. J Chem Phys 126 124114 (2007)
- What lessons can be learned from studying the folding of homologous proteins? Nickson AA, Clarke J. Methods 52 38-50 (2010)
- Flexibility and Disorder in Gene Regulation: LacI/GalR and Hox Proteins. Bondos SE, Swint-Kruse L, Matthews KS. J Biol Chem 290 24669-24677 (2015)
- The stability and dynamics of computationally designed proteins. Gonzalez NA, Li BA, McCully ME. Protein Eng Des Sel 35 gzac001 (2022)
Articles - 1enh mentioned but not cited (92)
- A comprehensive classification and evolutionary analysis of plant homeobox genes. Mukherjee K, Brocchieri L, Bürglin TR. Mol Biol Evol 26 2775-2794 (2009)
- Ab initio folding of proteins with all-atom discrete molecular dynamics. Ding F, Tsao D, Nie H, Dokholyan NV. Structure 16 1010-1018 (2008)
- ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions. Vitalis A, Pappu RV. J Comput Chem 30 673-699 (2009)
- Principal component analysis for protein folding dynamics. Maisuradze GG, Liwo A, Scheraga HA. J Mol Biol 385 312-329 (2009)
- Prediction of protein folding rates from the amino acid sequence-predicted secondary structure. Ivankov DN, Finkelstein AV. Proc Natl Acad Sci U S A 101 8942-8944 (2004)
- Solvent accessible surface area approximations for rapid and accurate protein structure prediction. Durham E, Dorr B, Woetzel N, Staritzbichler R, Meiler J. J Mol Model 15 1093-1108 (2009)
- A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary. Day R, Beck DA, Armen RS, Daggett V. Protein Sci 12 2150-2160 (2003)
- FOLD-RATE: prediction of protein folding rates from amino acid sequence. Gromiha MM, Thangakani AM, Selvaraj S. Nucleic Acids Res 34 W70-4 (2006)
- Architectures and functional coverage of protein-protein interfaces. Tuncbag N, Gursoy A, Guney E, Nussinov R, Keskin O. J Mol Biol 381 785-802 (2008)
- Application of the diffusion-collision model to the folding of three-helix bundle proteins. Islam SA, Karplus M, Weaver DL. J Mol Biol 318 199-215 (2002)
- Understanding ensemble protein folding at atomic detail. Hubner IA, Deeds EJ, Shakhnovich EI. Proc Natl Acad Sci U S A 103 17747-17752 (2006)
- Folding free energy function selects native-like protein sequences in the core but not on the surface. Jaramillo A, Wernisch L, Héry S, Wodak SJ. Proc Natl Acad Sci U S A 99 13554-13559 (2002)
- The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of Engrailed homeodomain. Religa TL, Johnson CM, Vu DM, Brewer SH, Dyer RB, Fersht AR. Proc Natl Acad Sci U S A 104 9272-9277 (2007)
- Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. He Y, Xiao Y, Liwo A, Scheraga HA. J Comput Chem 30 2127-2135 (2009)
- Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain. McCully ME, Beck DA, Daggett V. Biochemistry 47 7079-7089 (2008)
- Dynameomics: large-scale assessment of native protein flexibility. Benson NC, Daggett V. Protein Sci 17 2038-2050 (2008)
- Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins. Jayaram B, Bhushan K, Shenoy SR, Narang P, Bose S, Agrawal P, Sahu D, Pandey V. Nucleic Acids Res 34 6195-6204 (2006)
- High-resolution protein folding with a transferable potential. Hubner IA, Deeds EJ, Shakhnovich EI. Proc Natl Acad Sci U S A 102 18914-18919 (2005)
- Building native protein conformation from highly approximate backbone torsion angles. Gong H, Fleming PJ, Rose GD. Proc Natl Acad Sci U S A 102 16227-16232 (2005)
- Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles. Childers MC, Daggett V. J Phys Chem B 122 6673-6689 (2018)
- An all-atom force field for tertiary structure prediction of helical proteins. Herges T, Wenzel W. Biophys J 87 3100-3109 (2004)
- Computational protein design is a challenge for implicit solvation models. Jaramillo A, Wodak SJ. Biophys J 88 156-171 (2005)
- Fragment-HMM: a new approach to protein structure prediction. Li SC, Bu D, Xu J, Li M. Protein Sci 17 1925-1934 (2008)
- CK2 phosphorylation of the PRH/Hex homeodomain functions as a reversible switch for DNA binding. Soufi A, Noy P, Buckle M, Sawasdichai A, Gaston K, Jayaraman PS. Nucleic Acids Res 37 3288-3300 (2009)
- Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum. Schnieders MJ, Ponder JW. J Chem Theory Comput 3 2083-2097 (2007)
- Lanthanide-binding helix-turn-helix peptides: solution structure of a designed metallonuclease. Welch JT, Kearney WR, Franklin SJ. Proc Natl Acad Sci U S A 100 3725-3730 (2003)
- Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations. Sieradzan AK, Krupa P, Scheraga HA, Liwo A, Czaplewski C. J Chem Theory Comput 11 817-831 (2015)
- The N-terminus of the human RecQL4 helicase is a homeodomain-like DNA interaction motif. Ohlenschläger O, Kuhnert A, Schneider A, Haumann S, Bellstedt P, Keller H, Saluz HP, Hortschansky P, Hänel F, Grosse F, Görlach M, Pospiech H. Nucleic Acids Res 40 8309-8324 (2012)
- Critical nucleation size in the folding of small apparently two-state proteins. Bai Y, Zhou H, Zhou Y. Protein Sci 13 1173-1181 (2004)
- Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models. Stovgaard K, Andreetta C, Ferkinghoff-Borg J, Hamelryck T. BMC Bioinformatics 11 429 (2010)
- Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field. Kozłowska U, Maisuradze GG, Liwo A, Scheraga HA. J Comput Chem 31 1154-1167 (2010)
- Discriminative learning for protein conformation sampling. Zhao F, Li S, Sterner BW, Xu J. Proteins 73 228-240 (2008)
- Computational design and experimental verification of a symmetric protein homodimer. Mou Y, Huang PS, Hsu FC, Huang SJ, Mayo SL. Proc Natl Acad Sci U S A 112 10714-10719 (2015)
- Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum. Mackereth CD, Arrowsmith CH, Edwards AM, McIntosh LP. Proc Natl Acad Sci U S A 97 6316-6321 (2000)
- A revised density function for molecular surface definition in continuum solvent models. Ye X, Wang J, Luo R. J Chem Theory Comput 6 1157-1169 (2010)
- Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States. Nguyen D, Hoffpauir ZA, Iwahara J. Biochemistry 56 5866-5869 (2017)
- Modeling disordered regions in proteins using Rosetta. Wang RY, Han Y, Krassovsky K, Sheffler W, Tyka M, Baker D. PLoS One 6 e22060 (2011)
- Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates. Qi X, Portman JJ. Proc Natl Acad Sci U S A 104 10841-10846 (2007)
- A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding. Toofanny RD, Jonsson AL, Daggett V. Biophys J 98 2671-2681 (2010)
- Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate. McCully ME, Beck DA, Fersht AR, Daggett V. Biophys J 99 1628-1636 (2010)
- UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling. Bhattacharya D, Cao R, Cheng J. Bioinformatics 32 2791-2799 (2016)
- Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation. Arnautova YA, Vorobjev YN, Vila JA, Scheraga HA. Proteins 77 38-51 (2009)
- Structure-Based Prediction of Protein-Folding Transition Paths. Jacobs WM, Shakhnovich EI. Biophys J 111 925-936 (2016)
- A free-energy approach for all-atom protein simulation. Verma A, Wenzel W. Biophys J 96 3483-3494 (2009)
- SeqRate: sequence-based protein folding type classification and rates prediction. Lin GN, Wang Z, Xu D, Cheng J. BMC Bioinformatics 11 Suppl 3 S1 (2010)
- A probabilistic and continuous model of protein conformational space for template-free modeling. Zhao F, Peng J, Debartolo J, Freed KF, Sosnick TR, Xu J. J Comput Biol 17 783-798 (2010)
- Investigation of homeodomain membrane translocation properties: insights from the structure determination of engrailed-2 homeodomain in aqueous and membrane-mimetic environments. Carlier L, Balayssac S, Cantrelle FX, Khemtémourian L, Chassaing G, Joliot A, Lequin O. Biophys J 105 667-678 (2013)
- Evaluating and optimizing computational protein design force fields using fixed composition-based negative design. Alvizo O, Mayo SL. Proc Natl Acad Sci U S A 105 12242-12247 (2008)
- Simple electrostatic model improves designed protein sequences. Zollars ES, Marshall SA, Mayo SL. Protein Sci 15 2014-2018 (2006)
- A Dynamic Hydrophobic Core and Surface Salt Bridges Thermostabilize a Designed Three-Helix Bundle. Nguyen C, Young JT, Slade GG, Oliveira RJ, McCully ME. Biophys J 116 621-632 (2019)
- BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles. Putnam DK, Weiner BE, Woetzel N, Lowe EW, Meiler J. Proteins 83 1500-1512 (2015)
- Benchmarks for flexible and rigid transcription factor-DNA docking. Kim R, Corona RI, Hong B, Guo JT. BMC Struct Biol 11 45 (2011)
- Correlation between evolutionary structural development and protein folding. Nagao C, Terada TP, Yomo T, Sasai M. Proc Natl Acad Sci U S A 102 18950-18955 (2005)
- PFDB: A standardized protein folding database with temperature correction. Manavalan B, Kuwajima K, Lee J. Sci Rep 9 1588 (2019)
- Creating a Homeodomain with High Stability and DNA Binding Affinity by Sequence Averaging. Tripp KW, Sternke M, Majumdar A, Barrick D. J Am Chem Soc 139 5051-5060 (2017)
- Improvement of structure-based potentials for protein folding by native and nonnative hydrogen bonds. Enciso M, Rey A. Biophys J 101 1474-1482 (2011)
- Specificity landscapes unmask submaximal binding site preferences of transcription factors. Bhimsaria D, Rodríguez-Martínez JA, Pan J, Roston D, Korkmaz EN, Cui Q, Ramanathan P, Ansari AZ. Proc Natl Acad Sci U S A 115 E10586-E10595 (2018)
- Toward a detailed understanding of search trajectories in fragment assembly approaches to protein structure prediction. Kandathil SM, Handl J, Lovell SC. Proteins 84 411-426 (2016)
- A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins. Pereira de Araujo AF, Onuchic JN. Proc Natl Acad Sci U S A 106 19001-19004 (2009)
- Critical Features of Fragment Libraries for Protein Structure Prediction. Trevizani R, Custódio FL, Dos Santos KB, Dardenne LE. PLoS One 12 e0170131 (2017)
- Dioxane contributes to the altered conformation and oligomerization state of a designed engrailed homeodomain variant. Hom GK, Lassila JK, Thomas LM, Mayo SL. Protein Sci 14 1115-1119 (2005)
- Iterative assembly of helical proteins by optimal hydrophobic packing. Wu GA, Coutsias EA, Dill KA. Structure 16 1257-1266 (2008)
- Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins. Pereira de Araújo AF, Gomes AL, Bursztyn AA, Shakhnovich EI. Proteins 70 971-983 (2008)
- Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain. McCully ME, Beck DA, Daggett V. Protein Eng Des Sel 26 35-45 (2013)
- Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape. Mouro PR, de Godoi Contessoto V, Chahine J, Junio de Oliveira R, Pereira Leite VB. Biophys J 111 287-293 (2016)
- Designing succinct structural alphabets. Li SC, Bu D, Gao X, Xu J, Li M. Bioinformatics 24 i182-9 (2008)
- Polymer uncrossing and knotting in protein folding, and their role in minimal folding pathways. Mohazab AR, Plotkin SS. PLoS One 8 e53642 (2013)
- Constraint Logic Programming approach to protein structure prediction. Dal Palù A, Dovier A, Fogolari F. BMC Bioinformatics 5 186 (2004)
- Intermediates in the protein folding process: a computational model. Roterman I, Konieczny L, Banach M, Jurkowski W. Int J Mol Sci 12 4850-4860 (2011)
- Multimolecule test-tube simulations of protein unfolding and aggregation. McCully ME, Beck DA, Daggett V. Proc Natl Acad Sci U S A 109 17851-17856 (2012)
- A firefly-inspired method for protein structure prediction in lattice models. Maher B, Albrecht AA, Loomes M, Yang XS, Steinhöfel K. Biomolecules 4 56-75 (2014)
- Bayesian inference of protein structure from chemical shift data. Bratholm LA, Christensen AS, Hamelryck T, Jensen JH. PeerJ 3 e861 (2015)
- Insights into the folding pathway of the Engrailed Homeodomain protein using replica exchange molecular dynamics simulations. Koulgi S, Sonavane U, Joshi R. J Mol Graph Model 29 481-491 (2010)
- Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction. Lipska AG, Seidman SR, Sieradzan AK, Giełdoń A, Liwo A, Scheraga HA. J Chem Phys 144 184110 (2016)
- Predicting the folding pathway of engrailed homeodomain with a probabilistic roadmap enhanced reaction-path algorithm. Li DW, Yang H, Han L, Huo S. Biophys J 94 1622-1629 (2008)
- The roles of entropy and kinetics in structure prediction. Bowman GR, Pande VS. PLoS One 4 e5840 (2009)
- Wavelet Analysis of Protein Motion. Benson NC, Daggett V. Int J Wavelets Multiresolut Inf Process 10 1250040 (2012)
- Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling. Rakhmanov SV, Makeev VJ. BMC Struct Biol 7 19 (2007)
- Characterization of protein folding by a Φ-value calculation with a statistical-mechanical model. Wako H, Abe H. Biophys Physicobiol 13 263-279 (2016)
- Evaluating amber force fields using computed NMR chemical shifts. Koes DR, Vries JK. Proteins 85 1944-1956 (2017)
- A critical analysis of computational protein design with sparse residue interaction graphs. Jain S, Jou JD, Georgiev IS, Donald BR. PLoS Comput Biol 13 e1005346 (2017)
- The aqueous environment as an active participant in the protein folding process. Gadzała M, Dułak D, Kalinowska B, Baster Z, Bryliński M, Konieczny L, Banach M, Roterman I. J Mol Graph Model 87 227-239 (2019)
- Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch. D'Amelio N, Tanielian B, Sadqi M, López-Navajas P, Muñoz V. Int J Mol Sci 23 2412 (2022)
- Diffusion-collision model algorithms for protein folding kinetics. Vasilkoski Z, Weaver DL. J Comput Chem 25 1101-1107 (2004)
- Error assessment in molecular dynamics trajectories using computed NMR chemical shifts. Koes DR, Vries JK. Comput Theor Chem 1099 152-166 (2017)
- Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection. Toofanny RD, Simms AM, Beck DA, Daggett V. BMC Bioinformatics 12 334 (2011)
- Native structure-based modeling and simulation of biomolecular systems per mouse click. Lutz B, Sinner C, Bozic S, Kondov I, Schug A. BMC Bioinformatics 15 292 (2014)
- Surface residues and nonadditive interactions stabilize a consensus homeodomain protein. Sternke M, Tripp KW, Barrick D. Biophys J 120 5267-5278 (2021)
- Thermostabilization mechanisms in thermophilic versus mesophilic three-helix bundle proteins. Nguyen C, Yearwood LM, McCully ME. J Comput Chem 43 197-205 (2022)
- Efficient conformational space exploration in ab initio protein folding simulation. Ullah A, Ahmed N, Pappu SD, Shatabda S, Ullah AZ, Rahman MS. R Soc Open Sci 2 150238 (2015)
- Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins. Lobanov MY, Pereyaslavets LB, Likhachev IV, Matkarimov BT, Galzitskaya OV. Comput Struct Biotechnol J 19 5960-5968 (2021)
- Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations. Wei H, Zhao Z, Luo R. J Chem Theory Comput 17 6214-6224 (2021)
Reviews citing this publication (10)
- Is there a unifying mechanism for protein folding? Daggett V, Fersht AR. Trends Biochem Sci 28 18-25 (2003)
- The present view of the mechanism of protein folding. Daggett V, Fersht A. Nat Rev Mol Cell Biol 4 497-502 (2003)
- Homeodomain interactions. Wolberger C. Curr Opin Struct Biol 6 62-68 (1996)
- Full-sequence computational design and solution structure of a thermostable protein variant. Shah PS, Hom GK, Ross SA, Lassila JK, Crowhurst KA, Mayo SL. J Mol Biol 372 1-6 (2007)
- Fast protein folding kinetics. Gelman H, Gruebele M. Q Rev Biophys 47 95-142 (2014)
- Analysis and design of three-stranded coiled coils and three-helix bundles. Schneider JP, Lombardi A, DeGrado WF. Fold Des 3 R29-40 (1998)
- Karyopherins in nuclear transport of homeodomain proteins during development. Ye W, Lin W, Tartakoff AM, Tao T. Biochim Biophys Acta 1813 1654-1662 (2011)
- Sequence 'minimization': exploring the sequence landscape with simplified sequences. Clarke ND. Curr Opin Biotechnol 6 467-472 (1995)
- Supramolecular Architectures of Nucleic Acid/Peptide Hybrids. Higashi SL, Rozi N, Hanifah SA, Ikeda M. Int J Mol Sci 21 E9458 (2020)
- MOLS sampling and its applications in structural biophysics. Ramya L, Nehru Viji S, Arun Prasad P, Kanagasabai V, Gautham N. Biophys Rev 2 169-179 (2010)
Articles citing this publication (62)
- The complete folding pathway of a protein from nanoseconds to microseconds. Mayor U, Guydosh NR, Johnson CM, Grossmann JG, Sato S, Jas GS, Freund SM, Alonso DO, Daggett V, Fersht AR. Nature 421 863-867 (2003)
- Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation. Piper DE, Batchelor AH, Chang CP, Cleary ML, Wolberger C. Cell 96 587-597 (1999)
- Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Mayor U, Johnson CM, Daggett V, Fersht AR. Proc Natl Acad Sci U S A 97 13518-13522 (2000)
- Solution structure of a protein denatured state and folding intermediate. Religa TL, Markson JS, Mayor U, Freund SM, Fersht AR. Nature 437 1053-1056 (2005)
- SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA. Kipp M, Göhring F, Ostendorp T, van Drunen CM, van Driel R, Przybylski M, Fackelmayer FO. Mol Cell Biol 20 7480-7489 (2000)
- Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures. Fraenkel E, Rould MA, Chambers KA, Pabo CO. J Mol Biol 284 351-361 (1998)
- Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity. Hirsch JA, Aggarwal AK. EMBO J 14 6280-6291 (1995)
- Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. Zhao X, Sun M, Zhao J, Leyva JA, Zhu H, Yang W, Zeng X, Ao Y, Liu Q, Liu G, Lo WH, Jabs EW, Amzel LM, Shan X, Zhang X. Am J Hum Genet 80 361-371 (2007)
- The denatured state of Engrailed Homeodomain under denaturing and native conditions. Mayor U, Grossmann JG, Foster NW, Freund SM, Fersht AR. J Mol Biol 333 977-991 (2003)
- Covariation of residues in the homeodomain sequence family. Clarke ND. Protein Sci 4 2269-2278 (1995)
- Solution structure of the Grb2 N-terminal SH3 domain complexed with a ten-residue peptide derived from SOS: direct refinement against NOEs, J-couplings and 1H and 13C chemical shifts. Wittekind M, Mapelli C, Lee V, Goldfarb V, Friedrichs MS, Meyers CA, Mueller L. J Mol Biol 267 933-952 (1997)
- Prediction of amino acid sequence from structure. Raha K, Wollacott AM, Italia MJ, Desjarlais JR. Protein Sci 9 1106-1119 (2000)
- Achieving stability and conformational specificity in designed proteins via binary patterning. Marshall SA, Mayo SL. J Mol Biol 305 619-631 (2001)
- Global optimization and folding pathways of selected alpha-helical proteins. Carr JM, Wales DJ. J Chem Phys 123 234901 (2005)
- Electrostatics significantly affect the stability of designed homeodomain variants. Marshall SA, Morgan CS, Mayo SL. J Mol Biol 316 189-199 (2002)
- Computational design of co-assembling protein-DNA nanowires. Mou Y, Yu JY, Wannier TM, Guo CL, Mayo SL. Nature 525 230-233 (2015)
- Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms. Wensley BG, Gärtner M, Choo WX, Batey S, Clarke J. J Mol Biol 390 1074-1085 (2009)
- Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera. Ke A, Wolberger C. Protein Sci 12 306-312 (2003)
- NMR and temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics. Gillespie B, Vu DM, Shah PS, Marshall SA, Dyer RB, Mayo SL, Plaxco KW. J Mol Biol 330 813-819 (2003)
- Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan. Nanda V, Brand L. Proteins 40 112-125 (2000)
- Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein. DeMarco ML, Alonso DO, Daggett V. J Mol Biol 341 1109-1124 (2004)
- The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site. Baird-Titus JM, Clark-Baldwin K, Dave V, Caperelli CA, Ma J, Rance M. J Mol Biol 356 1137-1151 (2006)
- Cooperative folding of a protein mini domain: the peripheral subunit-binding domain of the pyruvate dehydrogenase multienzyme complex. Spector S, Kuhlman B, Fairman R, Wong E, Boice JA, Raleigh DP. J Mol Biol 276 479-489 (1998)
- Free-energy landscape of the villin headpiece in an all-atom force field. Herges T, Wenzel W. Structure 13 661-668 (2005)
- Isolation of mutations that disrupt cooperative DNA binding by the Drosophila bicoid protein. Burz DS, Hanes SD. J Mol Biol 305 219-230 (2001)
- MNX1 (HLXB9) mutations in Currarino patients. Garcia-Barceló MM, Lui VC, So MT, Miao X, Leon TY, Yuan ZW, Ngan ES, Ehsan T, Chung PH, Khong PL, Wong KK, Tam PK. J Pediatr Surg 44 1892-1898 (2009)
- A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. Beck DA, Daggett V. Biophys J 93 3382-3391 (2007)
- Molecular interactions of the γ-clade homeodomain-leucine zipper class I transcription factors during the wheat response to water deficit. Harris JC, Sornaraj P, Taylor M, Bazanova N, Baumann U, Lovell B, Langridge P, Lopato S, Hrmova M. Plant Mol Biol 90 435-452 (2016)
- NMR studies of the pbx1 TALE homeodomain protein free in solution and bound to DNA: proposal for a mechanism of HoxB1-Pbx1-DNA complex assembly. Jabet C, Gitti R, Summers MF, Wolberger C. J Mol Biol 291 521-530 (1999)
- Folding of the KIX domain: characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Schanda P, Brutscher B, Konrat R, Tollinger M. J Mol Biol 380 726-741 (2008)
- Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif. McLaughlin WA, Berman HM. J Mol Biol 330 43-55 (2003)
- Experimental and Computational Analysis of Protein Stabilization by Gly-to-d-Ala Substitution: A Convolution of Native State and Unfolded State Effects. Zou J, Song B, Simmerling C, Raleigh D. J Am Chem Soc 138 15682-15689 (2016)
- Comparison of multiple crystal structures with NMR data for engrailed homeodomain. Religa TL. J Biomol NMR 40 189-202 (2008)
- Preprocessing of rotamers for protein design calculations. Shah PS, Hom GK, Mayo SL. J Comput Chem 25 1797-1800 (2004)
- Roles of conformational disorder and downhill folding in modulating protein-DNA recognition. Chu X, Muñoz V. Phys Chem Chem Phys 19 28527-28539 (2017)
- The DNA binding specificity of engrailed homeodomain. Draganescu A, Tullius TD. J Mol Biol 276 529-536 (1998)
- A phage display selection of engrailed homeodomain mutants and the importance of residue Q50. Simon MD, Sato K, Weiss GA, Shokat KM. Nucleic Acids Res 32 3623-3631 (2004)
- Novel structural features in two ZHX homeodomains derived from a systematic study of single and multiple domains. Bird LE, Ren J, Nettleship JE, Folkers GE, Owens RJ, Stammers DK. BMC Struct Biol 10 13 (2010)
- The solution structure of the homeodomain of the rat insulin-gene enhancer protein isl-1. Comparison with other homeodomains. Ippel H, Larsson G, Behravan G, Zdunek J, Lundqvist M, Schleucher J, Lycksell PO, Wijmenga S. J Mol Biol 288 689-703 (1999)
- Cross-talk between the paired domain and the homeodomain of Pax3: DNA binding by each domain causes a structural change in the other domain, supporting interdependence for DNA Binding. Apuzzo S, Abdelhakim A, Fortin AS, Gros P. J Biol Chem 279 33601-33612 (2004)
- Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins. Ganesan SJ, Matysiak S. J Chem Theory Comput 10 2569-2576 (2014)
- Binding regularities in complexes of transcription factors with operator DNA: homeodomain family. Chirgadze YN, Zheltukhin EI, Polozov RV, Sivozhelezov VS, Ivanov VV. J Biomol Struct Dyn 26 687-700 (2009)
- APL: An angle probability list to improve knowledge-based metaheuristics for the three-dimensional protein structure prediction. Borguesan B, Barbachan e Silva M, Grisci B, Inostroza-Ponta M, Dorn M. Comput Biol Chem 59 Pt A 142-157 (2015)
- Binding polymorphism in the DNA bound state of the Pdx1 homeodomain. Babin V, Wang D, Rose RB, Sagui C. PLoS Comput Biol 9 e1003160 (2013)
- Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation. Nasedkin A, Marcellini M, Religa TL, Freund SM, Menzel A, Fersht AR, Jemth P, van der Spoel D, Davidsson J. PLoS One 10 e0125662 (2015)
- Two-state folding over a weak free-energy barrier. Favrin G, Irbäck A, Samuelsson B, Wallin S. Biophys J 85 1457-1465 (2003)
- Atomistic molecular dynamics simulations of bioactive engrailed 1 interference peptides (EN1-iPeps). Gandhi NS, Blancafort P, Mancera RL. Oncotarget 9 22383-22397 (2018)
- Geometry optimization for peptides and proteins: comparison of Cartesian and internal coordinates. Koslover EF, Wales DJ. J Chem Phys 127 234105 (2007)
- Structural guided scaffold phage display libraries as a source of bio-therapeutics. Man YK, DiCara D, Chan N, Vessillier S, Mather SJ, Rowe ML, Howard MJ, Marshall JF, Nissim A. PLoS One 8 e70452 (2013)
- Using Molecular Dynamics Simulations as an Aid in the Prediction of Domain Swapping of Computationally Designed Protein Variants. Mou Y, Huang PS, Thomas LM, Mayo SL. J Mol Biol 427 2697-2706 (2015)
- Engineered lanthanide-binding metallohomeodomains: designing folded chimeras by modular turn substitution. Lim S, Franklin SJ. Protein Sci 15 2159-2165 (2006)
- Prediction of the three-dimensional structure of proteins using the electrostatic screening model and hierarchic condensation. Avbelj F, Fele L. Proteins 31 74-96 (1998)
- REMD and umbrella sampling simulations to probe the energy barrier of the folding pathways of engrailed homeodomain. Jani V, Sonavane UB, Joshi R. J Mol Model 20 2283 (2014)
- A Boundary-Integral Approach for the Poisson-Boltzmann Equation with Polarizable Force Fields. Cooper CD. J Comput Chem 40 1680-1692 (2019)
- Continuous representations of proteins: construction of coordinate models from curvature profiles. Hausrath AC, Goriely A. J Struct Biol 158 267-281 (2007)
- Photo-control of DNA binding by an engrailed homeodomain-photoactive yellow protein hybrid. Kumar A, Ali AM, Woolley GA. Photochem Photobiol Sci 14 1729-1736 (2015)
- Traversing the folding pathway of proteins using temperature-aided cascade molecular dynamics with conformation-dependent charges. Jani V, Sonavane U, Joshi R. Eur Biophys J 45 463-482 (2016)
- Macromolecular Crystallography and Structural Biology Databases at NIST. Gilliland GL. J Res Natl Inst Stand Technol 106 1155-1173 (2001)
- Nature-inspired engineering of an artificial ligase enzyme by domain fusion. Tong CL, Kanwar N, Morrone DJ, Seelig B. Nucleic Acids Res 50 11175-11185 (2022)
- Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants. Špačková N, Trošanová Z, Šebesta F, Jansen S, Burda JV, Srb P, Zachrdla M, Žídek L, Kozelka J. Phys Chem Chem Phys 20 12664-12677 (2018)
- Rapid Evolution of the Embryonically Expressed Homeobox Gene LEUTX within Primates. Lewin TD, Blagrove JR, Holland PWH. Genome Biol Evol 15 evad097 (2023)
- Role of PI(4,5)P2 and Cholesterol in Unconventional Protein Secretion. Joliot A. Adv Exp Med Biol 1422 381-392 (2023)
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