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Journal of Chemical Theory and Computation, ISSN 1549-9618, 05/2017, Volume 13, Issue 5, p. 2123
We present a new conceptually simple and computationally efficient method for nonlinear normal-mode analysis called NOLB. It relies on the... 
Proteins | Deformation | Graphical user interface | Nonlinear analysis | Eigenvalues | Angular velocity | Rigid blocks | Biopolymers | Translations | Molecular chains | Deoxyribonucleic acid--DNA
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 08/2016, Volume 56, Issue 8, p. 1410
  Here we address the problem of the assignment of atom types and bond orders in low molecular weight compounds. For this purpose, we have developed a... 
Molecules | Errors | Atoms & subatomic particles | Software
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 10/2015, Volume 55, Issue 10, p. 2242
  Selection of putative binding poses is a challenging part of virtual screening for protein-protein interactions. Predictive models to filter out binding... 
Proteins | Interfaces | Binding sites | Optimization
Journal Article
Bioinformatics (Oxford, England), ISSN 1367-4803, 06/2019, pp. 1 - 24
Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion... 
Bioinformatics | Machine Learning | Image Processing | Computer Science
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 05/2014, Volume 35, Issue 12, pp. 950 - 956
Journal Article
Journal Article
Journal Article
Journal of Computer-Aided Molecular Design, ISSN 0920-654X, 11/2019
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 10/2019, Volume 40, Issue 27, pp. 2391 - 2399
In this study, we propose a novel optimization algorithm, with application to the refinement of molecular complexes. Particularly, we consider optimization... 
energy landscape | rigid‐body modeling | molecular docking | structural optimization | PROTEIN DOCKING | rigid-body modeling | ENERGY MINIMIZATION | KNOWLEDGE | FORCE-FIELD | CHARMM | CHEMISTRY, MULTIDISCIPLINARY | PROGRAM | Models | Algorithms | Mathematical optimization | Analysis | Protein binding | Computational Physics | Bioinformatics | Physics | Computer Science
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 05/2017, Volume 13, Issue 5, pp. 2123 - 2134
Journal Article
BIOINFORMATICS, ISSN 1367-4803, 08/2019, Volume 35, Issue 16, pp. 2801 - 2808
Motivation: Protein quality assessment (QA) is a crucial element of protein structure prediction, a fundamental and yet open problem in structural... 
SELECTION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | PREDICTION | Bioinformatics | Computer Science
Journal Article
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 08/2016, Volume 56, Issue 8, pp. 1410 - 1419
Journal Article
Science, ISSN 0036-8075, 06/2017, Volume 356, Issue 6342, pp. eaah6345 - eaah6345
One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases, parts of two-component... 
HAMP DOMAIN | CHEMORECEPTORS | NITRATE | COGNATE TRANSDUCER | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI K-12 | ASPARTATE RECEPTOR | MEMBRANE-PROTEINS | NARX | DISULFIDE CROSS-LINKING | RHODOPSIN II | Signal Transduction | Membrane Proteins - genetics | Models, Molecular | Escherichia coli Proteins - metabolism | Phosphoproteins - genetics | Escherichia coli - chemistry | Phosphoproteins - metabolism | Phosphoproteins - chemistry | Membrane Proteins - chemistry | Escherichia coli - metabolism | Escherichia coli Proteins - genetics | Protein Domains | Membrane Proteins - metabolism | Escherichia coli Proteins - chemistry | Crystallization - methods | High resolution | Hydrogen | Virulence | Control systems | Segments | Nitrates | Biochemistry | Kinases | Antiinfectives and antibacterials | Hydrogen bonding | Fragmentation | Proteins | Signal transduction | Microorganisms | E coli | Sporulation | Bacteria | Sensors | Atomic structure | Bonding | Symmetry | Binding | Pathogens | Cell survival | Crystallization | Antimicrobial agents | Metabolism | Chemotaxis | Survival | Displacement | Histidine kinase | Pathogenicity | Amplification | Phototaxis | Asymmetry | Ligands | Environment | Detection | Chemoreceptors | Receptors | Histidine | Helices | Crystal structure | Life Sciences | Modeling and Simulation | Biological Physics | Biochemistry, Molecular Biology | Computer Science | Biomolecules | Physics
Journal Article
ONCOTARGET, ISSN 1949-2553, 08/2017, Volume 8, Issue 32, pp. 53730 - 53739
Elenagen is a plasmid encoding p62/SQSTM1, the first DNA vaccine possessing two mutually complementing mechanisms of action: it elicits immune response against... 
IMMUNE-RESPONSE | FEASIBILITY | cancer vaccine | CANCER-RELATED INFLAMMATION | CYCLOPHOSPHAMIDE | PROGNOSTIC SCORE | breast cancer | SIGNALING ADAPTER P62 | chemotherapy | EPITHELIAL OVARIAN-CANCER | CELL BIOLOGY | BREAST-CANCER | ovary cancer | cancer immunotherapy | TUMORIGENESIS
Journal Article
Bioinformatics, ISSN 1367-4803, 09/2019, Volume 35, Issue 18, pp. 3313 - 3319
Abstract Motivation Protein model quality assessment (QA) is a crucial and yet open problem in structural bioinformatics. The current best methods for... 
PREDICTOR | SCORE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Signal and Image Processing | Bioinformatics | Statistics | Machine Learning | Computer Science
Journal Article
Bioinformatics, ISSN 1367-4803, 12/2018, Volume 34, Issue 23, pp. 4046 - 4053
Abstract Motivation The computational prediction of a protein structure from its sequence generally relies on a method to assess the quality of protein models.... 
SCORING FUNCTION | MODELS | FORCE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | PREDICTION | ACCURACY | Quantitative Biology - Biomolecules | Bioinformatics | Machine Learning | Artificial Intelligence | Computer Science
Journal Article