*  EMBOSS: aaindexextract
T Empirical predictions of protein conformation J Ann. Rev. Biochem. 47, 251-276 (1978) C PALJ810106 0.977 TANS770110 0.956 ... Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng ... Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino acid indices for prediction of protein structure and ... Protein Eng. 2, 93-100 (1988). [UI:89221001] *Tomii, K. and Kanehisa, M.; ...
  http://emboss.sourceforge.net/apps/release/6.2/emboss/apps/aaindexextract.html
*  NMR paper Effects of fluorophore attachment on protein conformation and dynamics studied by spFRET and NMR. - BioNMR
Effects of fluorophore attachment on protein conformation and dynamics studied by spFRET and NMR. Related Articles Effects of ... NMR paper] Insights into conformation and dynamics of protein GB1 during folding and unfolding b Insights into conformation and ... Effects of fluorophore attachment on protein conformation and dynamics studied by spFRET and NMR.. Related Articles Effects of ... Related Articles Insights into conformation and dynamics of protein GB1 during folding and unfolding by NMR. J Mol Biol. 2004 ...
  http://www.bionmr.com/forum/journal-club-9/effects-fluorophore-attachment-protein-conformation-dynamics-studied-spfret-nmr-24932/
*  DynDom - Protein Domain Motions
You can use DynDom if you have two conformations of the same protein. These may be two X-ray structures, or structures ... DynDom is a program that determines protein domains, hinge axes and amino acid residues involved in the hinge bending. It is ...
  http://fizz.cmp.uea.ac.uk/dyndom/dyndomWhen.jsp
*  enzymes - General Biology Discussion
Variability in conformation among different protein molecules is important since conformation is critical in being able to bind ... Variability in conformation among different protein molecules is important since conformation is critical in being able to bind ... The way proteins are structured, you have so many conformations (recall 4 levels of structure) possible depending on ... The way proteins are structured, you have so many conformations (recall 4 levels of structure) possible depending on ...
  http://www.protocol-online.org/biology-forums/posts/10755.html
*  Evolving L-Systems to Capture Protein Structure Native Conformations | SpringerLink
In this state, proteins show repeated substructures like alpha helices and beta sheet ... A protein is a linear chain of amino acids that folds into a unique functional structure, called its native state. ... Unger, I., Moult, J.: Finding the lowest free energy conformation of a protein is an NP-hard problem: Proof and implications. ... Patton, A., Punch, W., Goodman, E.: A Standard GA approach to native protein conformation prediction. In: Proceedings of the ...
  https://link.springer.com/chapter/10.1007%2F978-3-540-31989-4_7
*  Understanding Enzymes: Protein Conformation Coupled Catalysis
The role of conformational changes in enzyme catalysis will be discussed. A model will be advanced consisting of conformational ensembles and multiple reaction pathways to explain the incredible catalytic efficiency of enzymes. The results of ensemble and single-molecule experiments obtained with dihydrofolate reductase will be presented that support this model ...
  https://smartech.gatech.edu/handle/1853/32761
*  Detecting intermediate protein conformations using algebraic topology | BMC Bioinformatics | Full Text
At every iteration a parent protein conformation is chosen from the conformation pool, then a rotatable bond between two C- α ... For each selected protein, the C- α based representation of the start and target points are used to obtain the conformations ... Therefore, the search space made out of all possible conformations that a protein can assume is large and its enumeration is ... Shehu A, Olson B. Guiding the search for native-like protein conformations with an ab-initio tree-based exploration. Int J ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1918-z
*  Gas-phase hydrogen/deuterium exchange in a travelling wave ion guide for the examination of protein conformations
We conclude that HDX of protein ions in a TWIG is highly sensitive to protein conformation, enables the detection of conformers ... Accumulating evidence suggests that solution-phase conformations of small globular proteins and large molecular protein ... protein charge state) influence part a, the gas-phase conformation of the protein influence part b. ... The conformations revealed in these short times should better reflect the conformational landscape of protein ions at the ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2794942/
*  "Protein conformation in a vaccine matters" by Trudy G. Morrison
Our results demonstrate that the conformation of antigens in VLPs is of critical importance for optimal stimulation of ... protein conformation, respiratory syncytial virus, vaccine, fusion protein ... Morrison, Trudy G., "Protein conformation in a vaccine matters" (2015). Open Access Articles. 2612. https://escholarship. ... Our results demonstrate that the conformation of antigens in VLPs is of critical importance for optimal stimulation of ...
  https://escholarship.umassmed.edu/oapubs/2612/
*  Publication | Laboratory for Protein Conformation Diseases | RIKEN
An infectious conformation compatible with two highly divergent yeast prion proteins. Cell 121, 49-62 (2005). ... Tanaka, M. A protein transformation protocol for introducing yeast prion particles into yeast. Methods in Enzymology (Guide to ... Nekooki-Machida, Y., Kurosawa, M., Nukina, N., Ito, K., Oda, T., and Tanaka, M. Distinct conformations of in vitro and in vivo ... Ohhashi, Y., Ito, K., Toyama, B.H., Weissman, J.S., and Tanaka M. Differences in prion strain conformations result from non- ...
  http://www.motomasalab.brain.riken.jp/pub_eng.html
*  HDX Solution - HDX Solution - unlock insights in protein structure conformation | Bruker
The Bruker HDX Solution enables you to answer these questions and unlock insights into protein structure conformation, ... Do you want to understand more about the protein-ligand (drug/protein) interactions and their relationship to drug activity? ... monitor protein/protein-drug interactions and perform epitope mapping. In recent years Hydrogen Deuterium Exchange Mass ... technique within the arsenal of analytical tools available for providing such insights into protein structure conformation. ...
  https://www.bruker.com/it/products/mass-spectrometry-and-separations/hdx-solution/overview.html
*  RCSB PDB - 1A13: G PROTEIN-BOUND CONFORMATION OF MASTOPARAN-X, NMR, 14 STRUCTURES Methods Report Page
G protein-bound conformation of mastoparan-X: heteronuclear multidimensional transferred nuclear overhauser effect analysis of ...
  http://www.rcsb.org/pdb/explore/materialsAndMethods.do?structureId=1A13
*  Protofold: A Successive Kinetostatic Compliance Method for Protein Conformation Prediction | Journal of Mechanical Design |...
Protofold: A Successive Kinetostatic Compliance Method for Protein Conformation Prediction Kazem Kazerounian, Khalid Latif and ... Kazerounian K, Latif K, Alvarado C. Protofold: A Successive Kinetostatic Compliance Method for Protein Conformation Prediction ... Return to: Protofold: A Successive Kinetostatic Compliance Method for Protein Conformation Prediction ... the final conformation of the protein. This methodology is implemented in a computer software package named PROTOFOLD . In this ...
  http://mechanicaldesign.asmedigitalcollection.asme.org/article.aspx?articleid=1448578
*  Lysine Acetylation Controls Local Protein Conformation by Influencing Proline Isomerization - Oxford Neuroscience
trans conformation and reduces K4me3. Environmental stress-induced genes are most sensitive to the changes atK14 influencing H3 ... tail conformation and K4me3. By contrast, ribosomal protein genes maintain K4me3, required for their repression during stress, ... Lysine Acetylation Controls Local Protein Conformation by Influencing Proline Isomerization Howe FS., Boubriak I., Sale MJ., ... trans conformation and reduces K4me3. Environmental stress-induced genes are most sensitive to the changes atK14 influencing H3 ...
  https://www.neuroscience.ox.ac.uk/publications/506203
*  Effects of Protein Conformation in Docking: Improved Pose Prediction Through Protein Pocket Adaptation - Certara
Computational methods for docking ligands have been shown to be remarkably dependent on precise protein conformation, where ... Effects of Protein Conformation in Docking: Improved Pose Prediction Through Protein Pocket Adaptation. ...
  https://www.certara.com/citations/effects-of-protein-conformation-in-docking-improved-pose-prediction-through-protein-pocket-adaptation/
*  SuperBiHelix method for predicting the pleiotropic ensemble of G-protein-coupled receptor conformations | PNAS
2011) Bihelix: Towards de novo structure prediction of an ensemble of G-protein coupled receptor conformations. Proteins 80(2): ... the crystal conformation for each helix must be in that helix's top 36 conformations. The ranking of the crystal conformation ... We rely on energy ordering the final set of conformations without ligand or G protein and there could be too many nonactive ... SuperBiHelix method for predicting the pleiotropic ensemble of G-protein-coupled receptor conformations. Jenelle K. Bray, ...
  http://www.pnas.org/content/111/1/E72
*  The Bioactive Protein-Ligand Conformation of GluN2C-Selective Positive Allosteric Modulators Bound to the NMDA Receptor |...
The Bioactive Protein-Ligand Conformation of GluN2C-Selective Positive Allosteric Modulators Bound to the NMDA Receptor. Thomas ... The Bioactive Protein-Ligand Conformation of GluN2C-Selective Positive Allosteric Modulators Bound to the NMDA Receptor ... Protein-Ligand Complex of PYD-106 Bound to GluN2C. Thomas M. Kaiser, Steven A. Kell, Hirofumi Kusumoto, Gil Shaulsky, Subhrajit ... Protein-Ligand Complex of PYD-106 Bound to GluN2C. Thomas M. Kaiser, Steven A. Kell, Hirofumi Kusumoto, Gil Shaulsky, Subhrajit ...
  http://molpharm.aspetjournals.org/content/93/2/141
*  "Influenza A M2 Protein Conformation Depends On Choice Of Model Membran" by Kei Saotome , '11, Krisna C. Duong-Ly , '05 et al.
... optimistically may be considered conformations that are sampled by the protein at various stages during influenza infectivity. ... Here we show using site-directed spin-label EPR spectroscopy (SDSL-EPR) that the conformations of M2 peptides in membrane ... Altering the bilayer thickness or the lateral pressure profile within the bilayer membrane changes the M2 conformation observed ... The multiple M2 peptide conformations observed here, and in other published studies, ...
  http://works.swarthmore.edu/fac-chemistry/175/
*  Video: Yael Mandel-Gutfreund, "The role of RNA conformation in RNA-protein recognition"
The role of RNA conformation in RNA-protein recognition. ... Advances and Challenges in Protein-RNA: Recognition, Regulation ... The role of RNA conformation in RNA-protein recognition. Yael Mandel-Gutfreund, Video: The role of RNA conformation in RNA- ... Yael Mandel-Gutfreund, The role of RNA conformation in RNA-protein recognition, Advances and Challenges in Protein-RNA: ... Yael Mandel-Gutfreund, Video: The role of RNA conformation in RNA-protein recognition ...
  http://www.birs.ca/events/2015/5-day-workshops/15w5063/videos/watch/201506111139-Mandel-Gutfreund.html
*  Inverse Agonists: Tools to Reveal Ligand-Specific Conformations of G Protein-Coupled Receptors | Science Signaling
Inverse Agonists: Tools to Reveal Ligand-Specific Conformations of G Protein-Coupled Receptors ... Inverse Agonists: Tools to Reveal Ligand-Specific Conformations of G Protein-Coupled Receptors ... Inverse Agonists: Tools to Reveal Ligand-Specific Conformations of G Protein-Coupled Receptors ... Inverse Agonists: Tools to Reveal Ligand-Specific Conformations of G Protein-Coupled Receptors ...
  http://stke.sciencemag.org/content/2004/215/pe1
*  Designing interactions by control of protein-ligand complex conformation: tuning arginine-arene interaction geometry for...
Designing interactions by control of protein-ligand complex conformation: tuning arginine-arene interaction geometry for ... Designing interactions by control of protein-ligand complex conformation: tuning arginine-arene interaction geometry for ... as the proper choice of arginine-aromatic interacting partners opens up for ligand-controlled protein conformation that in turn ... d Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden ...
  http://pubs.rsc.org/en/content/articlelanding/2017/sc/c7sc04749e
*  Tracking flavin conformations in protein crystal structures with Raman spectroscopy and QM/MM calculations. - Semantic Scholar
Tracking flavin conformations in protein crystal structures with Raman spectroscopy and QM/MM calculations.' by Åsmund K Røhr ... Tracking flavin conformations in protein crystal structures with Raman spectroscopy and QM/MM calculations.. @article{ ... Tracking flavin conformations in protein crystal structures with Raman spectroscopy and QM/MM calculations.}, author={{\AA} ... Modulation of the flavin-protein interactions in NADH peroxidase and mercuric ion reductase: a resonance Raman study. *Julie ...
  https://www.semanticscholar.org/paper/Tracking-flavin-conformations-in-protein-crystal-R%C3%B8hr-Hersleth/d89b3e945fd1bc792de4bd98e6c8f512cc909940
*  Extracellular Matrix Heparan Sulfate Proteoglycans - Amyloid Proteins: The Beta Sheet Conformation and Disease - Neame - Wiley...
Neame, P. J. and Gallagher, J. T. (2005) Extracellular Matrix Heparan Sulfate Proteoglycans, in Amyloid Proteins: The Beta ... Sheet Conformation and Disease (ed J. D. Sipe), Wiley-VCH Verlag GmbH, Weinheim, Germany. doi: 10.1002/9783527619344.ch7 ...
  http://onlinelibrary.wiley.com/doi/10.1002/9783527619344.ch7/references
*  Lee CS[Author] - PubMed - NCBI
Avoiding Energy Loss on TADF Emitters: Controlling the Dual Conformations of D-A Structure Molecules Based on the Pseudoplanar ... Protein Database. *Reference Sequence (RefSeq). *All Proteins Resources.... *Sequence Analysis*BLAST (Basic Local Alignment ...
  https://www.ncbi.nlm.nih.gov/pubmed?term=Lee%20CS%5BAuthor%5D&cauthor=true&cauthor_uid=15635067
*  Prostaglandin 2 biosynthesis and metabolism Pathway Map - PrimePCR | Life Science | Bio-Rad
The productive conformation of prostaglandin G2 at the peroxidase site of prostaglandin endoperoxide H synthase: docking, ... Engineering of a protein with cyclooxygenase and prostacyclin synthase activities that converts arachidonic acid to ... The productive conformation of prostaglandin G2 at the peroxidase site of prostaglandin endoperoxide H synthase: docking, ... Engineering of a protein with cyclooxygenase and prostacyclin synthase activities that converts arachidonic acid to ...
  http://www.bio-rad.com/en-us/prime-pcr-assays/pathway/prostaglandin-2-biosynthesis-metabolism-fm