*  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
*  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
*  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/
*  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
*  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/
*  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
*  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
*  "Representing protein native states using weighted conformation ensembl" by Vijay Vammi
In the first part of the thesis, we focus on representing the native state of a given protein using a weighted ensemble ... The work described in this thesis focuses on methods used to construct such ensemble representations of proteins. A careful ... To incorporate dynamics into structural representations, ensembles of conformations, instead of a single structure, are used ... while capturing the dynamics of the protein that a single average structure misses. Using Ubiquitin as an example, we show that ...
  https://lib.dr.iastate.edu/etd/14461/
*  Conservation of Topology, But Not Conformation, of the Proteolipid Proteins of the Myelin Sheath | Journal of Neuroscience
... the myelin basic proteins and the proteolipid proteins (DM-20/PLP). The myelin basic proteins are extrinsic membrane proteins ... The proteolipid protein gene products DM-20 and PLP are adhesive intrinsic membrane proteins that make up ≥50% of the protein ... Curiously, changes in protein conformation imparted by the PLP-specific peptide not only confer sensitivity to amino acid ... Conservation of Topology, But Not Conformation, of the Proteolipid Proteins of the Myelin Sheath. Alexander Gow, Alexander ...
  http://www.jneurosci.org/content/17/1/181.long
*  Sequence Similarity - 3RRT: Structure of the RSV F protein in the post-fusion conformation Sequence Similarity Report...
Structure of respiratory syncytial virus fusion glycoprotein in the postfusion conformation reveals preservation of ... Fusion glycoprotein F0 protein, length: 84 (BLAST) Sequence Similarity Cutoff. Rank. Chains in Cluster. Cluster ID / Name. ... Fusion glycoprotein F0 protein, length: 374 (BLAST) Sequence Similarity Cutoff. Rank. Chains in Cluster. Cluster ID / Name. ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ...
  http://www.rcsb.org/pdb/explore/sequenceCluster.do?structureId=3RRT
*  Effect of Rearing Program, Body Conformation and Protein Level of...
The effect of pullet growth curve on body conformation and subsequent reproductive performance and effect of breeder feed ... protein level on reproductive performance was determined. The cost effec... ... Feeding a LO-protein diet resulted in feed cost savings. The feed cost of SD reared hens fed LO-protein diet was $0.03227 per ... Effect of Rearing Program, Body Conformation and Protein Level of Breeder Feed on Broiler Breeder Hen Reproductive Performance ...
  http://free-journal.umm.ac.id/detail-3864-title-effect-of-rearing-program-body-conformation-and-protein-level-of-breeder-feed-on-broiler-breeder-hen-reproductive-performance.html
*  Conformation-dependent recognition of a protein by T cells requires presentation without processing | Biochemical Journal
It should then be expected that T-cell recognition of protein antigens in vitro will be independent of protein conformation. ... Conformation-dependent recognition of a protein by T cells requires presentation without processing. M Z Atassi, G S Bixler Jr ... The exquisite dependency of the recognition by the clones on the conformation of the protein antigen and their ability to ... Conformation-dependent recognition of a protein by T cells requires presentation without processing ...
  http://www.biochemj.org/content/259/3/731
*  4q2g » Phosphatidate cytidylyltransferase, conformation 2 - Orientations of Proteins in Membranes (OPM) database
Localization: Bacterial Gram-negative inner membrane (516 proteins). 4q2g » Phosphatidate cytidylyltransferase, conformation 2 ... 4q2g » Phosphatidate cytidylyltransferase, conformation 2. 3D view in Jmol or Webmol Download Coordinates Topology in Bacterial ...
  http://opm.phar.umich.edu/protein.php?pdbid=4q2g
*  Ole Lund - DTU
Glycosylation and protein conformation Hansen, Jan ; Lund, Ole ; Rapacki, Khristoffer ; Mosekilde, Erik ; Nielsen, Jens O. ; ... part of: Protein Structure by Distance Analysis (ISBN: 9051991614), pages: 247-254, 1994, IOS PressVan Diemenstraat 94, 1013 CN ... Presented at: Symposium on Distance Based Approaches to Protein Structure Determination, 1993, Lyngby ...
  http://www.dtu.dk/english/Service/Phonebook/Person?fr=1&id=5094&mr=10&peer=0&ptype=lbr&qt=dtupublicationquery&tab=2
*  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