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Structure, ISSN 0969-2126, 06/2019, Volume 27, Issue 6, pp. 1034 - 1040.e3
Flexibility is often a key determinant of protein function. To elucidate the link between their molecular structure and role in an organism, computational... 
deep learning | autoencoder | protein docking | molecular dynamics | molecular modeling | Proteins | Molecular dynamics | Neural networks | Analysis
Journal Article
Nature, ISSN 0028-0836, 2014, Volume 510, Issue 7503, pp. 172 - 175
Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments(1-7) and that lipids... 
MYCOBACTERIUM-TUBERCULOSIS | ATOM FORCE-FIELD | MOLECULAR-DYNAMICS | MULTIDISCIPLINARY SCIENCES | COMPLEXES | PURIFICATION | ION-CHANNEL | MOBILITY-MASS SPECTROMETRY | MODEL | MSCL | WATER | Apoproteins - chemistry | Cardiolipins - pharmacology | Protein Unfolding - drug effects | Protein Conformation - drug effects | Aquaporins - chemistry | Bacterial Proteins - chemistry | Substrate Specificity | Crystallography, X-Ray | Membrane Lipids - chemistry | Cation Transport Proteins - metabolism | Protein Folding - drug effects | Mass Spectrometry | Mycobacterium tuberculosis - chemistry | Membrane Proteins - metabolism | Ion Channels - chemistry | Phosphatidylglycerols - metabolism | Apoproteins - metabolism | Ammonia - metabolism | Models, Molecular | Aquaporins - metabolism | Escherichia coli Proteins - metabolism | Cardiolipins - metabolism | Escherichia coli - chemistry | Cardiolipins - chemistry | Phosphatidylglycerols - chemistry | Ion Channels - metabolism | Membrane Proteins - chemistry | Protein Stability - drug effects | Membrane Lipids - metabolism | Phosphatidylglycerols - pharmacology | Bacterial Proteins - metabolism | Membrane Lipids - pharmacology | Lipid Bilayers - chemistry | Cation Transport Proteins - chemistry | Escherichia coli Proteins - chemistry | Biological research | Physiological aspects | Lipids | Cooperative binding (Biochemistry) | Research | Structure | Molecular biology | Membrane proteins | Biology, Experimental | Proteins | Studies | Membranes | E coli | Binding sites | Crystal structure
Journal Article
ISSN 0003-2654, 12/2015, Volume 141, Issue 1, pp. 7 - 75
We present EM∩IM, software that allows the calculation of collision cross-sections from electron density maps obtained for example by means of transmission... 
Journal Article
Structure, ISSN 0969-2126, 07/2013, Volume 21, Issue 7, pp. 1097 - 1106
Proteins often assemble in multimeric complexes to perform a specific biologic function. However, trapping these high-order conformations is difficult... 
Proteins | Constraints | Mathematical models | Swarm intelligence | Flexibility | Flexible structures | Assembly | Optimization
Journal Article
Structure, ISSN 0969-2126, 07/2013, Volume 21, Issue 7, pp. 1097 - 1106
Journal Article
Analyst (Cambridge UK), ISSN 0003-2654, 12/2015, Volume 141, Issue 1, pp. 70 - 75
We present EM member of M, software that allows the calculation of collision cross-sections from electron density maps obtained for example by means of... 
Maps | Ionic mobility | Software | Electron density | Atomic structure | Mass spectrometry | Cross sections | Computer programs
Journal Article
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, ISSN 1549-9618, 09/2019, Volume 15, Issue 9, pp. 5135 - 5143
Predicting the assembly of multiple proteins into specific complexes is critical to understanding their biological function in an organism and thus the design... 
REFINEMENT | SIDE-CHAIN | SERVER | COMPLEXES | FLEXIBILITY | ENSEMBLES | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | OPTIMIZATION | COMPLEMENTARITY | Proteins | Binding | Chains | Docking | Representations | Electrostatics
Journal Article
Nature Communications, ISSN 2041-1723, 2017, Volume 8, Issue 1, pp. 2033 - 9
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 08/2013, Volume 9, Issue 8, pp. 3515 - 3526
We present a new generation of coarse-grained (CG) potentials that account for a simplified electrostatic description of soluble proteins. The treatment of... 
DYNAMICS SIMULATIONS | RECOGNITION | SEQUENCES | WATER-SOLUBLE ANALOG | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | FORCE-FIELD | SOLVENT MODEL | ALGORITHMS | STRUCTURAL DYNAMICS | NUCLEIC-ACIDS | BETA
Journal Article
Analyst, ISSN 0003-2654, 01/2016, Volume 141, Issue 1, pp. 70 - 75
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 07/2016, Volume 113, Issue 29, p. 8230
  Bovine cytochrome c oxidase is an integral membrane protein complex comprising 13 protein subunits and associated lipids. Dimerization of the complex has... 
Proteins | Phosphorylation | Membranes | Lipids | Mass spectrometry
Journal Article
The Analyst, ISSN 0003-2654, 01/2016, Volume 141, Issue 1, pp. 70 - 75
We present EM∩IM, software that allows the calculation of collision cross-sections from electron density maps obtained for example by means of transmission... 
Image Processing, Computer-Assisted | Microscopy, Electron - methods | Models, Molecular | Protein Conformation | Software | Proteins - chemistry | Statistics as Topic - methods | Mass Spectrometry - methods | Electrons
Journal Article
Scientific Reports, ISSN 2045-2322, 2017, Volume 7, Issue 1, pp. 235 - 9
Predicting the structure of large molecular assemblies remains a challenging task in structural biology when using integrative modeling approaches. One of the... 
PROTEIN DOCKING | OPTIMIZATION | MAPS | MULTIDISCIPLINARY SCIENCES | ARCHITECTURES | COMPLEXES | Models, Molecular | Computational Biology - methods | Macromolecular Substances - chemistry | Macromolecules | Fitness
Journal Article
Journal Article