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Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-35909-2
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- Article
Unleashing the potential of noncanonical amino acid biosynthesis to create cells with precision tyrosine sulfation.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-33111-4
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- Article
Erratum: A universal origin for secondary relaxations in supercooled liquids and structural glasses.
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- Nature Physics, 2015, v. 11, n. 3, p. 287, doi. 10.1038/nphys3286
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A universal origin for secondary relaxations in supercooled liquids and structural glasses.
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- Nature Physics, 2010, v. 6, n. 1, p. 62, doi. 10.1038/nphys1432
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The shapes of cooperatively rearranging regions in glass-forming liquids.
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- Nature Physics, 2006, v. 2, n. 4, p. 268, doi. 10.1038/nphys261
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The hinge-bending mode in lysozyme.
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- Nature, 1976, v. 262, n. 5566, p. 325, doi. 10.1038/262325a0
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- Article
Exploring chromosomal structural heterogeneity across multiple cell lines.
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- eLife, 2020, p. 1, doi. 10.7554/eLife.60312
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- Article
Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics.
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- Nucleic Acids Research, 2016, v. 44, n. W1, p. W256, doi. 10.1093/nar/gkw304
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- Article
Protein frustratometer: a tool to localize energetic frustration in protein molecules.
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- Nucleic Acids Research, 2012, v. 40, p. W348, doi. 10.1093/nar/gks447
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FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations.
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- Bioinformatics, 2021, v. 37, n. 18, p. 3038, doi. 10.1093/bioinformatics/btab176
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- Article
Local energetic frustration conservation in protein families and superfamilies.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-43801-2
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- Article
Discrete Kinetic Models from Funneled Energy Landscape Simulations.
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- PLoS ONE, 2012, v. 7, n. 12, p. 1, doi. 10.1371/journal.pone.0050635
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- Article
The role of atomic level steric effects and attractive forces in protein folding.
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- Proteins, 2012, v. 80, n. 2, p. 362, doi. 10.1002/prot.23187
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Optimizing physical energy functions for protein folding.
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- Proteins, 2004, v. 54, n. 1, p. 88, doi. 10.1002/prot.10429
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Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides.
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- Proteins, 1999, v. 34, n. 3, p. 281, doi. 10.1002/(SICI)1097-0134(19990215)34:3<281::AID-PROT2>3.0.CO;2-2
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Protein Folding Mechanisms and the Multidimensional Folding Funnel
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- Proteins, 1998, v. 32, n. 2, p. 136
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Quantum simulation of ferrocytochrome c.
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- Nature, 1988, v. 334, n. 6184, p. 726, doi. 10.1038/334726a0
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- Article
Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level.
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- Biomolecules (2218-273X), 2019, v. 9, n. 2, p. 77, doi. 10.3390/biom9020077
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- Article
Energy landscape underlying spontaneous insertion and folding of an alpha-helical transmembrane protein into a bilayer.
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- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07320-9
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- Article
Modeling the therapeutic efficacy of NFκB synthetic decoy oligodeoxynucleotides (ODNs).
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- BMC Systems Biology, 2018, v. 12, p. 1, doi. 10.1186/s12918-018-0525-6
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- Article
A structural dynamics model for how CPEB3 binding to SUMO2 can regulate translational control in dendritic spines.
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- PLoS Computational Biology, 2022, v. 18, n. 11, p. 1, doi. 10.1371/journal.pcbi.1010657
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- Article
A generalized Flory-Stockmayer kinetic theory of connectivity percolation and rigidity percolation of cytoskeletal networks.
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- PLoS Computational Biology, 2022, v. 18, n. 5, p. 1, doi. 10.1371/journal.pcbi.1010105
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- Article
A simple statistical field theory of heteropolymer collapse with application to protein folding.
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- Biopolymers, 1990, v. 30, n. 1/2, p. 177, doi. 10.1002/bip.360300117
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On the Number of Metastable States in a Stripe Glass.
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- International Journal of Modern Physics B: Condensed Matter Physics; Statistical Physics; Applied Physics, 2001, v. 15, n. 24/25, p. 3292, doi. 10.1142/S0217979201007646
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Funnels, pathways, and the energy landscape of protein folding: A synthesis.
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- Proteins, 1995, v. 21, n. 3, p. 167, doi. 10.1002/prot.340210302
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The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein.
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- PLoS Computational Biology, 2010, v. 6, n. 7, p. 1, doi. 10.1371/journal.pcbi.1000835
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- Article
The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures.
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- PLoS Computational Biology, 2008, v. 4, n. 5, p. 1, doi. 10.1371/journal.pcbi.1000070
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The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain.
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- FASEB Journal, 2005, v. 19, n. 11, p. 1389, doi. 10.1096/fj.04-3590hyp
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OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations.
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- PLoS Computational Biology, 2021, v. 17, n. 2, p. 1, doi. 10.1371/journal.pcbi.1008308
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Frustration in biomolecules.
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- Quarterly Reviews of Biophysics, 2014, v. 47, n. 4, p. 285, doi. 10.1017/S0033583514000092
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Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model.
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- Journal of Biological Physics, 2022, v. 48, n. 1, p. 37, doi. 10.1007/s10867-021-09596-3
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The physics and bioinformatics of binding and folding-an energy landscape perspective.
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- Biopolymers, 2003, v. 68, n. 3, p. 333, doi. 10.1002/bip.10286
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Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families.
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- Nucleic Acids Research, 2024, v. 52, n. W1, p. W233, doi. 10.1093/nar/gkae244
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- Article
Single-molecule conformational dynamics of a transcription factor reveals a continuum of binding modes controlling association and dissociation.
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- Nucleic Acids Research, 2021, v. 49, n. 19, p. 11211, doi. 10.1093/nar/gkab874
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The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome.
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- Nucleic Acids Research, 2021, v. 49, n. D1, p. D172, doi. 10.1093/nar/gkaa818
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AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes.
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- Nucleic Acids Research, 2020, v. 48, n. W1, p. W25, doi. 10.1093/nar/gkaa356
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Folding funnels: The key to robust protein structure prediction.
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- Journal of Computational Chemistry, 2002, v. 23, n. 1, p. 138, doi. 10.1002/jcc.1162
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Resolving the fine structure in the energy landscapes of repeat proteins.
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- QRB Discovery, 2022, v. 3, p. 1, doi. 10.1017/qrd.2022.4
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Learning To Fold Proteins Using Energy Landscape Theory.
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- Israel Journal of Chemistry, 2014, v. 54, n. 8/9, p. 1311, doi. 10.1002/ijch.201300145
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Protein structure prediction: making AWSEM AWSEM-ER by adding evolutionary restraints.
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- Proteins, 2017, v. 85, n. 11, p. 2127, doi. 10.1002/prot.25367
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A fresh glass of frozen chaos.
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- Nature, 1996, v. 382, n. 6591, p. 495, doi. 10.1038/382495a0
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Surveying biomolecular frustration at atomic resolution.
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- Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-19560-9
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- Article
Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.
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- Protein Science: A Publication of the Protein Society, 2016, v. 25, n. 1, p. 255, doi. 10.1002/pro.2751
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