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Topic: Protein structure prediction

Ads by Google      ExPASy - Tools Jpred - A consensus method for protein secondary structure prediction at University of Dundee [ Protein identification and characterization ] [ DNA -> Protein ] [ Similarity searches ] [ Pattern and profile searches ] [ Post-translational modification prediction ] [ Topology prediction ] [ Primary structure analysis ] [ Secondary structure prediction ] [ Tertiary structure ] [ Sequence alignment ] [ Biological text analysis ] - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides) http://www.expasy.ch/tools      Skolnick Group Publications Skolnick, What practical use is protein structure prediction to drug discovery? Skolnick and A. Kolinski, De Novo Prediction of Protein Tertiary Structure. Proteins: Structure, Function and Genetics, 44, 133-149 (2001) http://www.bioinformatics.buffalo.edu/current_buffalo/skolnick/publications.html      HMG-D protein - DNA complex As a tool for theoretical prediction of the structure, we have chosen molecular dynamics (MD) simulations which our group has used already as a powerful method for bridging experimental and theoretical studies of protein-DNA complexes. We have recognized a trial complex of the HMG box with TATA--DNA as best stabilized, most consistent with the experimental data, and, thus, most probably corresponding to the real structure of the complex. The refinement will be carried out to verify our predicted structure and to demonstrate the validity of our method. http://www.ks.uiuc.edu/Research/pro_DNA/hmgd   (748 words)      ExPASy - Tools Jpred - A consensus method for protein secondary structure prediction at University of Dundee [Protein identification and characterization] [DNA -> Protein] [Similarity searches] [Pattern and profile searches] [Post-translational modification prediction] [Topology prediction] [Primary structure analysis] [Secondary structure prediction] [Tertiary structure] [Sequence alignment] [Phylogenetic analysis] [Biological text analysis] SAPS - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI] http://www.expasy.org/tools   (2122 words)      A Guide to Structure Prediction See the clickable flowchart to see what I think is a generalised approach to predicting protein structure. The pretty alignment shown in the secondary structure prediction section was drawn using Geoff Barton's ALSCRIPT program. Mostly, however, there are links within the other sections that can give you more information about them. http://speedy.embl-heidelberg.de/gtsp   (685 words)      YourArt.com >> Encyclopedia >> memory It may be that short-term memory is supported by transient changes in neuronal communication, whereas long-term memories are maintained by more stable and permanent changes in neural structure that are dependent on protein synthesis. Although traditional studies of memory began in the realms of philosophy, the late nineteenth and early twentieth century put memory within the paradigms of cognitive psychology. Brain areas such as the hippocampus, the amygdala, or the mammillary bodies are thought to be involved in certain kinds of memory. http://www.yourart.com/research/encyclopedia.cgi?subject=/memory   (1899 words)      Structure Prediction Biomolecular Modelling Group, Imperial Cancer Research Fund, UK Protein secondary structure prediction, Baylor College of Medicine, USA. Predictions of secondary structures and inside/outside properties of residues at each position in an aligned sequences are based on generalized rules for globular proteins, which are derived from observations of known 3D-structure of proteins. Secondary structure prediction using the procedure defined by Garnier, Osguthorpe and Robson, 1978 http://cgat.ukm.my/spores/Predictory/sporulate/structure_prediction.html   (1228 words)      Characterisation of protein families The principal methods utilised are comparisons of protein structures, multiple sequence alignments, molecular modelling, prediction of structures and direct primary structure determinations. The research programme aims at understanding of structure-function relationships among different protein families. The techniques also allow predictions of the membrane protein sidedness, i.e. http://www.mbb.ki.se/forsk/bpn.html   (1228 words)      A Hybrid Algorithm for Determining Protein Structure [4] J.-F. Gibrat, J. Garnier, and B. Robson, "Further Developments of Protein Secondary Structure Prediction Using Information Theory," J. [28] R.H. Lathrop, T.A. Webster, and T.F. Smith, "Ariadne: Pattern-Directed Inference and Hierarchical Abstraction in Protein Structure Recognition," Comm. This hybrid system improves its ability to determine how amino acid sequences fold into 3D protein structures. http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/mags/ex/&toc=comp/mags/ex/1994/04/x4toc.xml&DOI=10.1109/64.336147   (687 words)      SWBIC - Transmembrane Prediction [Brunel University] "The PSIPRED protein structure prediction server allows you to submit a protein sequence, perform a prediction of your choice, and receive the results of the prediction via E-mail. You may select one of three prediction methods to apply to your sequence: PSIPRED - a highly accurate secondary structure prediction method, MEMSAT 2 - a new version of our widely used transmembrane topology prediction method, and GenTHREADER - a new sequence profile based fold recognition method." [ISREC] Predicts transmembrane regions and orientation using a combination of several weight-matrices. http://www.swbic.org/links/1.12.8.php   (139 words)      Accelrys: Scientific References: Accelrys Staff Papers 1990 - 1999 Frank J.J. Leusen, Steffen Wilke, Paul Verwer and Gerhard E. Engel, Computational approaches to crystal structure and polymorph prediction, in 'Implications of Molecular and Materials Structure for New Technologies' (Eds.: Judith A.K. Howard, Frank H. Allen and Gregory P. Shields), NATO Science Series E, Volume 360, Kluwer Academic Publishers, Dordrecht, The Netherlands, pp. Souchet, M. Legave, N. Jullian, H.-O. Bertrand, A. Bril, and I. Berrebi-Bertrand, Structure of the human glycogen-associated protein phosphatase 1 regulatory subunit hGM: homology modeling revealed an (alpha/beta)8-barrel-like fold in the multidomain protein, Protein Science (1999), 8, p. Fitzgerald and R.J. Bartlett, "Optimum structures and vibrational frequencies of (SiC)2 clusters," Intern. http://www.accelrys.com/reference/refs/staff_1990_1999.html   (9575 words)      publications list   Chemical shift dispersion and secondary structure prediction in unfolded and partly-folded proteins.   Insights into the structure and dynamics of unfolded proteins from NMR. Two different neurodegenerative diseases caused by proteins with similar structures. http://www.scripps.edu/mb/dyson/publications_list.htm   (9575 words)      Proteomics and protein biochemistry Tools include: [Protein identification and characterization] [DNA -> Protein] [Similarity searches] [Pattern and profile searches] [Post-translational modification prediction] [Topology prediction] [Primary structure analysis] [Secondary structure... Protocols The following protocols are available in PDF format: Isotope Coded Affinity Tag Reagents Acid Cleavable ICAT Labelling Prot... http://www.biowww.net/browse.php?cat=5   (204 words)      Proteins: Biogenesis to Degradation - Virtual Library of Biochemistry & Cell Biology See also the Carbohydrates and Glycosylation page for more information on protein glycosylation and the Structure and Function Prediction Servers section of the Structural Biology page for post-translational modification and other sequence-based prediction servers. The Ubiquitin System for Protein Modification and Degradation - A broad range of information on the ubiquitin/proteasome pathway. Protein Degradation Resource - Information on cytosolic and lysosomal protein degradation pathways. http://www.biochemweb.org/proteins.shtml   (751 words)      521-322 Protein Biochemistry and Proteomics The content will include modern biochemistry methods and database analysis for characterising protein structure, function and expression; experiments that emphasise aspects of protein unfolding, determination and analysis of ligand binding data; and the use of computers in the analysis and prediction of protein structure. Special requirements: Before the commencement of the semester, students must advise the Department of Biochemistry and Molecular Biology of their order of preference for the alternative practical sessions and the other subjects they will be taking. Biochemistry and molecular biology 521-211, 521-212 and either 521-220 or 521-221; or 521-024; or 521-213 plus physiology 536-250. http://www.unimelb.edu.au/HB/2001/subjects/521-322.html   (253 words)      ON THE NUMBER OF STRUCTURAL FAMILIES IN THE PROTEIN UNIVERSE Such a big number of single-protein families is a serious limitation to the homology-based approach to protein structure prediction. Calculations of the number of structural families based on the probabilities of a new structure to belong to one of the previously known folds (formula 5), results into a surprisingly low number of protein families of about 700 (Figure 3). This difference we explain by biased nature of the PDB, representing mostly proteins which can be crystallized and are biologically interesting. http://www.bionet.nsc.ru/bgrs/thesis/100   (253 words)      Protein domain database: DOMO If the domain structure is unknown, the entry points to a composite secondary structural prediction obtained by different techniques such as PREDATOR (13), SIMPA96 (14), DSC (15), MAP123D (16), COILS (17), or TMAP (18). A major issue related to protein classification is the decomposition of biomolecules into their constituent structural domains typically defined as independent and globular folding units within a three-dimensional protein structure (1). Tertiary structural data which could guide a visual determination of such domain boundaries are missing for a vast majority of protein families. http://www.infobiogen.fr/services/domo   (1713 words)      Abstract - Design of a novel globular protein fold with atomic-level accuracy Here, we used a general computational strategy that iterates between sequence design and structure prediction to design a 93-residue alpha/beta protein called Top7 with a novel sequence and topology. A major challenge of computational protein design is the creation of novel proteins with arbitrarily chosen three-dimensional structures. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature. http://depts.washington.edu/bakerpg/abstracts/Kuhlman-Science-v302-p1364.html   (1713 words)      Membrane Protein Transmembrane Secondary Structure Prediction Server We have a list of other web servers for membrane protein secondary structure prediction. The purpose of this server is to predict the transmembrane (TM) secondary structures of membrane proteins, using the method of preference functions. Membrane protein sequence is the minimal input required by the prediction program. http://split.pmfst.hr/split/4   (1000 words)      SOSUI/submit a protein sequence SOSUI: classification and secondary structure prediction system for membrane proteins. Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system A theoretical method for distinguishing between soluble and membrane proteins http://sosui.proteome.bio.tuat.ac.jp/sosui_submit.html   (208 words)      A procedure for the prediction of temperature-sensitive mutants of a globular protein based solely on the amino acid sequence -- Varadarajan et al. 93 (24): 13908 -- Proceedings of the National Academy of Sciences that are likely to be buried in the protein structure. A procedure for the prediction of temperature-sensitive mutants of a globular protein based solely on the amino acid sequence -- Varadarajan et al. A procedure for the prediction of temperature-sensitive mutants of a globular protein based solely on the amino acid sequence http://www.pnas.org/cgi/content/abstract/93/24/13908   (208 words)      Protein Structure Prediction Center CASP experiments aim at establishing the current state of the art in protein structure prediction, identifying what progress has been made, and highlighting where future effort may be most productively focused. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. In addition to support of the CASP meetings our goal is to promote an objective evaluation of prediction methods on a continuing basis. http://predictioncenter.gc.ucdavis.edu   (232 words)      Biomolecular Engineering Rohl's research interests include protein structure prediction and protein engineering. Examples include protein engineering (the computational design of proteins to enhance or modify their functions), the development of sensors that integrate biomolecules with electronic components, and new laboratory devices and analytical tools for studying gene regulation, protein expression, and other complex biological systems. The pore itself is a naturally occurring bacterial toxin made of self-assembling protein molecules. http://currents.ucsc.edu/03-04/02-16/biomolecular.html   (729 words)      Analysis of Conformational Changes on Protein-Protein Complexes A final exhaustive analysis of the secondary structure elements involved on conformational changes is done, so a characterization of the different kind of structural movements among the different families of associated protein is proposed. However, computational methods for protein - protein prediction face the problem of the structuralflexibility of any of the components upon association. The aim of this last step is to search for protein regions (group of secondary strucrture elements) that remain invariable upon association in order to better understand the conformational changes. http://www.iscb.org/ismb2004/posters/raulATscmbb.ulb.ac.be_868.html   (227 words)      UCL Biochemistry Biocomputing Group The Biocomputing group comprises of researchers making use of computing and database resources to elucidate facets of protein function and structure. BTPRED - prediction of location and type of beta-turns in protein sequences. Atlas of Protein Side-Chain Interactions - analysis of sidechain-sidechain interaction geometries. http://www.biochem.ucl.ac.uk/bsm/biocomp   (355 words)      biolinks.htm Besides threading, it also interages some other sequence and structure prediction and analysis software around the world. A non-redundant protein database organized according to family relationships as defined collectively by ProSite patterns and PIR superfamilies. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of OWL. http://www.secsg.org/biolinks.htm   (655 words)      schedule.shtml Large scale genome analysis: from 3d structure prediction to the encyclopedia of life Mechanistic insights into the poly-phosphorylation of human SR proteins involved in splicing The Role of Protein Kinase A in Cyclic AMP- mediated Gene Expression in S49 Lymphoma Cells http://www.medicine.ucsd.edu/pharmaco/schedule.shtml   (655 words)      ApoLinks PSORT - prediction of protein sorting signals, Japan PDB - Protein Data Bank: 3-D biological macromolecular structure data Pfam - search for common protein domains in models for protein families http://www.celldeath.de/apolinks/apolinks.htm   (655 words)      IUL Biotechnology Series, Protein Structure Prediction, edited by Igor F. Tsigelny Chapters on concepts of protein structure prediction discuss areas such as a Bayesian approach to protein fold recognition, three-dimensional structure prediction using simplified structure models and Bayesian block fragments, and protein structure prediction using hidden Markov model structural libraries. field of protein structure prediction, where new approaches to fold recognition, structural alignment and threading continue to appear at a rate that leaves the individual investigator at a loss of which way to turn to solve any particular problem. Scientists developing prediction methods will find ideas here in descriptions of successful methods and programs in protein structure prediction. http://www.iul-press.us/Books/BBT03-Prediction/prediction.html   (453 words)      protein structure glossary high- throughput protein structure determination, protein structure prediction, protein structure technologies, structural genomics; Narrower terms quaternary protein structure, secondary protein structure, tertiary protein structure. Structure determination is easiest for single- domain proteins (and these are many of the ones that have been solved). The stated goal of structural genomics, as a field, involves generating a set of structures representative of most of the possible folds for specific protein domains and then solving the structures for new proteins based on known fold- structure relationships. http://www.genomicglossaries.com/content/protein_structure_glossary.asp   (453 words)

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