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PEP-FOLD3: faster denovo structure prediction for linear peptides in solution and in complex.
- Published in:
- Nucleic Acids Research, 2016, v. 44, n. W1, p. W449, doi. 10.1093/nar/gkw329
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- Publication type:
- Article
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides.
- Published in:
- Nucleic Acids Research, 2012, v. 40, p. W288, doi. 10.1093/nar/gks419
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- Publication type:
- Article
PEP-FOLD: an online resource for de novo peptide structure prediction.
- Published in:
- Nucleic Acids Research, 2009, v. 37, n. suppl_2, p. W498, doi. 10.1093/nar/gkp323
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- Publication type:
- Article
In silico structural characterization of protein targets for drug development against Trypanosoma cruzi.
- Published in:
- Journal of Molecular Modeling, 2016, v. 22, n. 10, p. 1, doi. 10.1007/s00894-016-3115-9
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- Publication type:
- Article
Density functional conformational study of 2-O-sulfated 3,6 anhydro-α-D-galactose and of neo-κ- and ι-carrabiose molecules in gas phase and water.
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- Journal of Molecular Modeling, 2013, v. 19, n. 2, p. 893, doi. 10.1007/s00894-012-1621-y
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- Publication type:
- Article
Inhibitors of amyloid beta peptide aggregation: Toward new drugs against Alzheimer's disease.
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- Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2015, v. 11, n. 7, p. P352, doi. 10.1016/j.jalz.2015.06.235
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- Publication type:
- Article
Intrinsic Determinants of A&bgr;<sub>12-24</sub> pH-Dependent Self-Assembly Revealed by Combined Computational and Experimental Studies.
- Published in:
- PLoS ONE, 2011, v. 6, n. 9, p. 1, doi. 10.1371/journal.pone.0024329
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- Publication type:
- Article
Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent.
- Published in:
- Proteins, 2009, v. 75, n. 4, p. 954, doi. 10.1002/prot.22305
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- Publication type:
- Article
Targeting the early steps of Aβ16-22 protofibril disassembly by N-methylated inhibitors: A numerical study.
- Published in:
- Proteins, 2009, v. 75, n. 2, p. 442, doi. 10.1002/prot.22254
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- Publication type:
- Article
A coarse-grained protein force field for folding and structure prediction.
- Published in:
- Proteins, 2007, v. 69, n. 2, p. 394, doi. 10.1002/prot.21505
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- Publication type:
- Article
Aggregating the amyloid Aβ<sub>11-25</sub> peptide into a four-stranded β-sheet structure.
- Published in:
- Proteins, 2006, v. 65, n. 4, p. 877, doi. 10.1002/prot.21134
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- Article
Structures of soluble amyloid oligomers from computer simulations.
- Published in:
- Proteins, 2006, v. 65, n. 1, p. 180, doi. 10.1002/prot.21100
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- Publication type:
- Article
Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm.
- Published in:
- Proteins, 2005, v. 61, n. 4, p. 732, doi. 10.1002/prot.20698
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- Publication type:
- Article
The βαβαβ elementary supersecondary structure of the Rossmann fold from porcine lactate dehydrogenase exhibits characteristics of a molten globule.
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- Proteins, 2005, v. 60, n. 4, p. 740, doi. 10.1002/prot.20507
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- Publication type:
- Article
Complex folding pathways in a simple β-hairpin.
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- Proteins, 2004, v. 56, n. 3, p. 464, doi. 10.1002/prot.20127
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- Publication type:
- Article
Impact of the tail and mutations G131V and M129V on prion protein flexibility.
- Published in:
- Proteins, 2003, v. 51, n. 2, p. 258, doi. 10.1002/prot.10348
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- Publication type:
- Article
Computer simulations aimed at structure prediction of supersecondary motifs in proteins.
- Published in:
- Proteins, 2001, v. 45, n. 2, p. 159, doi. 10.1002/prot.1135
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- Publication type:
- Article
A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against Leishmania major.
- Published in:
- Bioinformatics & Biology Insights, 2017, n. 11, p. 1, doi. 10.1177/1177932217712471
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- Publication type:
- Article
Recent Computational Advances Regarding Amyloid-β and Tau Membrane Interactions in Alzheimer's Disease.
- Published in:
- Molecules, 2023, v. 28, n. 20, p. 7080, doi. 10.3390/molecules28207080
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- Publication type:
- Article
Effect of Cholesterol Molecules on Aβ1-42 Wild-Type and Mutants Trimers.
- Published in:
- Molecules, 2022, v. 27, n. 4, p. 1395, doi. 10.3390/molecules27041395
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- Publication type:
- Article
Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics.
- Published in:
- Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-52760-y
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- Publication type:
- Article
Hfq variant with altered RNA binding functions.
- Published in:
- Nucleic Acids Research, 2006, v. 34, n. 2, p. 709, doi. 10.1093/nar/gkj464
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- Publication type:
- Article
Evaluation of the coarse-grained OPEP force field for protein-protein docking.
- Published in:
- BMC Biophysics, 2016, v. 9, p. 1, doi. 10.1186/s13628-016-0029-y
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- Publication type:
- Article
Long timestep dynamics of peptides by the dynamics driver approach.
- Published in:
- Proteins, 1995, v. 21, n. 4, p. 282, doi. 10.1002/prot.340210403
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- Publication type:
- Article
Effect of urey-bradley-shimanouchi force field on the harmonic dynamics of proteins.
- Published in:
- Proteins, 1991, v. 11, n. 2, p. 120, doi. 10.1002/prot.340110205
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- Publication type:
- Article
A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35.
- Published in:
- PLoS Computational Biology, 2011, v. 7, n. 5, p. 1, doi. 10.1371/journal.pcbi.1002051
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- Publication type:
- Article
Substitutions at residue 211 in the prion protein drive a switch between CJD and GSS syndrome, a new mechanism governing inherited neurodegenerative disorders.
- Published in:
- Human Molecular Genetics, 2014, v. 23, n. 8, p. 2234, doi. 10.1093/hmg/ddt654
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- Publication type:
- Article
Substitutions at residue 211 in the prion protein drive a switch between CJD and GSS syndrome, a new mechanism governing inherited neurodegenerative disorders.
- Published in:
- Human Molecular Genetics, 2012, v. 21, n. 26, p. 5417, doi. 10.1093/hmg/dds377
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- Publication type:
- Article
Exposure of Von Willebrand Factor Cleavage Site in A1A2A3-Fragment under Extreme Hydrodynamic Shear.
- Published in:
- Polymers (20734360), 2021, v. 13, n. 22, p. 3912, doi. 10.3390/polym13223912
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- Publication type:
- Article
Structural characterization of VGVAPG, an elastin-derived peptide.
- Published in:
- Biopolymers, 2004, v. 76, n. 3, p. 266, doi. 10.1002/bip.20029
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- Publication type:
- Article
PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution.
- Published in:
- Nucleic Acids Research, 2023, v. 51, n. W1, p. W432, doi. 10.1093/nar/gkad376
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- Publication type:
- Article
A fast method for large-scale De Novo peptide and miniprotein structure prediction.
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- Journal of Computational Chemistry, 2010, v. 31, n. 4, p. 726, doi. 10.1002/jcc.21365
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- Article
Improved greedy algorithm for protein structure reconstruction.
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- Journal of Computational Chemistry, 2005, v. 26, n. 5, p. 506, doi. 10.1002/jcc.20181
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- Publication type:
- Article
Predicting helical hairpins from sequences by Monte Carlo simulations.
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- Journal of Computational Chemistry, 2000, v. 21, n. 7, p. 582, doi. 10.1002/(SICI)1096-987X(200005)21:7<582::AID-JCC7>3.0.CO;2-T
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- Publication type:
- Article
A vibrational molecular force field of model compounds with biological interest. IV. Parameters for the different glycosidic linkages of oligosaccharides.
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- Journal of Computational Chemistry, 1995, v. 16, n. 2, p. 188, doi. 10.1002/jcc.540160206
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- Article
A truncated Newton minimizer adapted for CHARMM and biomolecular applications.
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- Journal of Computational Chemistry, 1994, v. 15, n. 5, p. 532, doi. 10.1002/jcc.540150506
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- Publication type:
- Article
Vibrational molecular force field of model compounds with biologic interest. II. Harmonic dynamics of both anomers of glucose in the crystalline state.
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- Journal of Computational Chemistry, 1993, v. 14, n. 3, p. 263, doi. 10.1002/jcc.540140303
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- Publication type:
- Article
The use of ultraviolet resonance Raman intensities to test proposed molecular force fields for nucleic acid bases.
- Published in:
- Journal of Computational Chemistry, 1991, v. 12, n. 6, p. 731, doi. 10.1002/jcc.540120610
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- Publication type:
- Article
A vibrational molecular force field of model compounds with biological interest. I. Harmonic dynamics of crystalline urea at 123 K.
- Published in:
- Journal of Computational Chemistry, 1990, v. 11, n. 5, p. 560, doi. 10.1002/jcc.540110504
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- Publication type:
- Article
Evolution of large Aβ16–22 aggregates at atomic details and potential of mean force associated to peptide unbinding and fragmentation events.
- Published in:
- Proteins, 2023, v. 91, n. 8, p. 1152, doi. 10.1002/prot.26500
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- Publication type:
- Article
Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp.
- Published in:
- Chemistry - A European Journal, 2015, v. 21, n. 36, p. 12657, doi. 10.1002/chem.201500888
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- Publication type:
- Article
Breaking down cellulose fibrils with a mid-infrared laser.
- Published in:
- Cellulose, 2018, v. 25, n. 10, p. 5553, doi. 10.1007/s10570-018-1973-2
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- Publication type:
- Article
Epock: rapid analysis of protein pocket dynamics.
- Published in:
- 2015
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- Publication type:
- Product Review
Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation.
- Published in:
- Israel Journal of Chemistry, 2017, v. 57, n. 7/8, p. 564, doi. 10.1002/ijch.201600048
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- Publication type:
- Article