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Journal Article
Journal of Theoretical and Computational Chemistry, ISSN 0219-6336, 12/2012, Volume 11, Issue 6, pp. 1201 - 1215
We have investigated the folding of two helix-bundle proteins, 36-residue Villin headpiece and 56-residue E-domain of Staphylococcal protein A, by combining... 
Protein folding | GPU | coarse-graining | UNRES force field | HIERARCHICAL DESIGN | TESTS | FOLDING SIMULATIONS | POTENTIAL-ENERGY LANDSCAPE | MEAN FORCE | MODEL | GRAPHICS | CHEMISTRY, MULTIDISCIPLINARY | OPTIMIZATION | E-DOMAIN | VILLIN HEADPIECE SUBDOMAIN | Bundling | Proteins | Frames | Computer simulation | Molecular structure | Molecular dynamics | Deviation | Folding
Journal Article
Journal of computational chemistry, ISSN 0192-8651, 4/2010, Volume 31, Issue 6, pp. 1154 - 1167
Using the harmonic-approximation approach of the accompanying paper and AM1 energy surfaces of terminally-blocked amino-acid residues, we determined... 
protein folding | local-interaction potentials | harmonic approximation | molecular quantum mechanics | UNRES force field
Journal Article
The Journal of Physical Chemistry B, ISSN 1520-6106, 08/2018, Volume 122, Issue 34, pp. 8166 - 8173
The stability of DNA is crucial for the existence of most living organisms. Even a single DNA break can lead to serious problems, including cell death. In this... 
TRANSITION | REPAIR | CHROMATIN | UNRES FORCE-FIELD | CHEMISTRY, PHYSICAL | PREDICTIONS | SIMULATION | RADIATION | DAMAGE | EXPOSURE | TELOMERES
Journal Article
Journal of chemical theory and computation, ISSN 1549-9618, 03/2010, Volume 6, Issue 3, pp. 890 - 909
We report the implementation of our united-residue UNRES force field for simulations of protein structure and dynamics with massively parallel architectures.... 
protein folding | massively parallel computers | UNRES force field | fine-grained parallelism | Amdahl’s law
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 08/2019, Volume 123, Issue 34, pp. 7253 - 7269
Despite years of intensive research, little is known about oligomeric structures present during Alzheimer's disease (AD). Excess of amyloid beta (A beta)... 
FIBRIL FORMATION | OLIGOMER FORMATION | MECHANISM | UNRES FORCE-FIELD | ALZHEIMERS-DISEASE | AMYLOID-BETA(1-42) | CHEMISTRY, PHYSICAL | AMYLOID-BETA-PROTEIN | PEPTIDE AGGREGATION | REPLICA EXCHANGE | AQUEOUS-SOLUTION
Journal Article
Physical Review Letters, ISSN 0031-9007, 02/2013, Volume 110, Issue 9
A proposed coarse-grained model of nucleic acids demonstrates that average interactions between base dipoles, together with chain connectivity and... 
MOLECULAR-DYNAMICS | THERMODYNAMICS | PHYSICS, MULTIDISCIPLINARY | UNRES FORCE-FIELD | DNA | HYBRIDIZATION | SIMULATIONS | MODEL | EXCHANGE | POLYPEPTIDE | PREDICTION
Journal Article
Current Opinion in Structural Biology, ISSN 0959-440X, 2007, Volume 17, Issue 2, pp. 192 - 198
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 03/2017, Volume 146, Issue 12, p. 124106
A general and systematic method for the derivation of the functional expressions for the effective energy terms in coarse-grained force fields of polymer... 
LOCAL CONFORMATIONAL STATES | BIOMOLECULAR SYSTEMS | UNRES FORCE-FIELD | MEAN FORCE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | PROTEIN-STRUCTURE SIMULATIONS | OPTIMIZATION | AMINO-ACID RESIDUES | MODEL | ALPHA VIRTUAL BONDS | PREDICTION | Peptides - chemistry | Static Electricity | Thermodynamics
Journal Article