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Topic: Protein structure prediction

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	The Bioinformatics Center at Rensselaer and Wadsworth. Research -- Protein Structure Prediction
		Introduction: Prediction of protein structure is one of the most challenging fields of bioinformatics.
		Protein structure is important for various aspects of basic science and applied research on proteins.
		Bystroff, C. and Baker, D. Prediction of local structure in proteins using a library of sequence-structure motifs.
	www.bioinfo.rpi.edu /research/protein_structure_prediction.html (396 words)

	Protein structure prediction - Wikipedia, the free encyclopedia
		Protein structure prediction is one of the most significant technologies pursued by computational structural biology and theoretical chemistry.
		Despite community-wide efforts in structural genomics, the output of experimentally determined protein structures - typically by time-consuming and relatively expensive X-ray crystallography or NMR spectroscopy - is lagging far behind the output of protein sequences.
		The number of possible structures that proteins may possess is extremely large, as highlighted by the Levinthal paradox.
	en.wikipedia.org /wiki/Protein_structure_prediction (1161 words)

	MLNNg: Protein Structure Prediction (Site not responding. Last check: 2007-10-26)
		Even if the number of proteins whose primary sequence is known counts in the number of millions, only few thousands of them have been crystallized and their 3D structure deposited in the Protein Data Bank Unfortunately, neither alternative approaches based on nuclear magnetic resonance cannot be applied at the genomic scale.
		Prediction of disulfide bridges from sequence is thus one of the important (and difficult) tasks in structural genomics.
		In this way, the task of predicting the tertiary structure of a protein is splitted in two steps: initially a reliable predictor of secondary structure must be realized (here), then a predictor for the coarse-grained contact map can be used to identify contacts between the segments.
	www.dsi.unifi.it /neural/ProteinStructure/proteomics.html (1415 words)

	Rising accuracy of protein secondary structure prediction
		An extreme simplification is the prediction of protein structure in one dimension (1D), as represented by strings of, e.g., secondary structure, or residue solvent accessibility.
		The typical scenario in which secondary structure predictions help to learn about function are experts combining predictions and their intuition, most often to find similarities to proteins of known function but insignificant sequence similarity [196, 197, 40, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207].
		Protein secondary structure formation is influenced by long-range interactions [231, 46, 47] and by the environment [1, 232].
	cubic.bioc.columbia.edu /papers/2003_rev_dekker/paper.html (13505 words)

	Sisyphus and protein structure prediction
		Currently, databases for protein sequence (Bairoch and Apweiler, 1997) and protein structure (Bernstein et al., 1977) are expanding rapidly due to large scale sequencing projects (Oliver et al., 1992; Fleischmann et al., 1995; Fraser et al., 1995; Goffeau et al., 1996; Johnston et al., 1996) and improvements in experimental determination of 3D structures (Lattman, 1994).
		In contrast, the mean-force-potentials, derived from databases of protein structure (Sippl, 1990), attempt to describe the free-energy of the molecule.
		Native 3D structures of proteins are encoded by a linear sequence of amino acid residues.
	www.embl-heidelberg.de /~rost/Papers/sisyphus.html (8205 words)

	BioMed Central \| Full text \| Local protein structure prediction using discriminative models
		The quality of new fold predictions has risen significantly and in fold recognition incorporation of local structure predictions led to improvements in the accuracy of results.
		For secondary structure prediction this provision yielded a significant increase in performance [27].
		Profiles in the HSSP database were constructed for a given protein by aligning the sequence of the protein with homologous sequences and calculating an amino acid frequency profile.
	www.biomedcentral.com /1471-2105/7/14 (6726 words)

	Sisyphus and protein structure prediction
		The goal is to predict whether the residue at the centre of a segment of typically 13-21 adjacent residues is in a helix, strand or in none of the two (no regular secondary structure, often referred to as the 'coil' or 'loop' state).
		Various methods successfully use secondary structure predictions as a first step, e.g., prediction-based threading (indeed one of the problems of the Asilomar 1996 prediction contest was that many developers of threading algorithms used the same PHD secondary structure predictions as a first step), inter-strand, and inter-residue distance predictions.
		Fortunately, the prediction task is simplified by strong environmental constraints on transmembrane proteins: the lipid bilayer of the membrane reduces the degrees of freedom to such an extent that 3D structure formation becomes almost a 2D problem.
	cubic.bioc.columbia.edu /papers/pre1997_ismb/paper.html (16192 words)

	GMD Successful at a World-Wide Protein Structure Prediction Experiment
		A blind prediction is a structure prediction, for which the actual structure is not known at the time of the prediction, but will become available soon thereafter for evaluation.
		Here the structure prediction of the sequence in question is not based on a homologue among the structurally known proteins, most often because no such homologue exists.
		The goal is to predict the structure of the molecular complex consisting of the protein and the bound ligand.
	www.ercim.org /publication/Ercim_News/enw29/kramer.html (749 words)

	Protein Structure Prediction
		Single sequence-based prediction for coiled-coil regions using statistical patterns of coiled-coil proteins in the database.
		Prediction-based threading detecting the fold type and aligning a protein of unknown structure and a protein of known structure for low levels of sequence identity (< 25%).
		COILS Prediction of Coiled Coil Regions in Proteins
	cmgm.stanford.edu /WWW/www_predict.html (443 words)

	A Guide to Structure Prediction
		See the clickable flowchart to see what I think is a generalised approach to predicting protein structure.
		Pictures of protein three-dimensional structures were drawn using Suhail Islam's program PREPI (available from this server).
		The pretty alignment shown in the secondary structure prediction section was drawn using Geoff Barton's ALSCRIPT program.
	speedy.embl-heidelberg.de /gtsp (685 words)

	Tim Hubbard - Genome Analysis And Protein Structure Prediction
		I have worked on the development of algorithms for structure prediction, in particular algorithms to predict long range interactions directly from sequence, such as the pairing of
		I have co-organised the IBRM 'frontiers of structure prediction'
		Raphael Laplae has been developing tools to help evaluate the performance of sequence and structural alignment methods and Aroul Ramadass has just started a PhD and is currently investigating the evolution of protein sequences and structures.
	www.sanger.ac.uk /Teams/faculty/hubbard (508 words)

	UCSC HMM Applications Main Page (Site not responding. Last check: 2007-10-26)
		UCSC's SAM-T02 method for iterative SAM HMM construction and remote homology detection and protein structure prediction updates SAM-T99 by using predicted secondary structure information in its scoring functions.
		Submit a target protein sequence in FASTA format and receive SAM-T02 alignment, HMM, protein database query, secondary structure predictions, sequence logos and pairwise alignments of target to top database hits.
		SAM-T99 alignment, HMM, protein database query, and secondary structure prediction
	www.soe.ucsc.edu /research/compbio/HMM-apps (610 words)

	Protein Structure
		DSMP - Database of Structural Motifs in Proteins - CDFD (India)
		DSSP - Definitions of the Secondary Structures of Proteins Database - EMBL-Heidelberg (Germany)
		PDB-Select Database - is a Subset of the Structures of PDB entries containing (Non)-Homologous Sequences - EMBL-Heidelberg (Germany)
	restools.sdsc.edu /biotools/biotools9.html (1018 words)

	Protein Structure Prediction Center
		Our goal is to help advance the methods of identifying protein structure from sequence.
		In addition to support of the CASP meetings our goal is to promote an evaluation of prediction methods on a continuing basis.
		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.
	predictioncenter.gc.ucdavis.edu (174 words)

	PSA Structure Prediction
		The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence.
		Since we expect Web results to be more popular, we have made this the default for the "Return results via:" choice on the submission page; the standard e-mail delivery technique is still available as the other option for this choice.
		Analysis of full-length amino acid sequences that are assumed to be monomeric globular, water-soluble proteins consisting of a single domain.
	huxley.bu.edu /psa (196 words)

	Protein Structure Prediction Biotech Research
		protein protein structure threading icrf imperial cancer research fund prediction pssm sequence profiles solvation potential tertiary structure prediction protein structure prediction secondary structure fold gene genomics protein folding problem inverse folding lawrence kelley sawted
		bioinformatics gene analysis genome analysis bioinformatics tools threading secondary structure prediction fold prediction folding proteins protein protein structure prediction protein function prediction bioinformatics bioinfobank biology medicine poland europe
		Professional algorithmic and software solutions for the bioinformatics industry: PROSPECT for protein structure prediction, PatternHunter for identifying all approximate repeats in a complete genome, and COPIA for discovering motifs in a family of protein sequences
	www.onlinebiotech.com /research/protein-structure-prediction.html (193 words)

	PredictProtein - Structure Prediction and Sequence Analysis
		PredictProtein is a service for sequence analysis, structure and function prediction.
		When you submit any protein sequence PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure and function (more)
		Explicitly predicting normalized B-values enables the implicit identification of flexible and rigid regions that relate to protein function.
	www.predictprotein.org (297 words)

	Prediction of Protein Structure from Sequence
		FoldClass - predicts protein fold classes and protein domains
		NNSSP (prediction of protein secondary sturcture by nearest-neighbor algorithms)
		DAS (Dense Alignment Surface; prediction of transmembrane regions in proteins)
	www.cbs.dtu.dk /biolinks/pserve1.html (113 words)

	BCM Search Launcher: Protein Secondary Structure Prediction
		Coils - prediction of coiled coil regions (ISREC) [
		PSSP / SSP - segment-oriented prediction (Sanger) [
		TMpred - transmembrane region and orientation prediction (ISREC) [
	searchlauncher.bcm.tmc.edu /seq-search/struc-predict.html (164 words)

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