> Tag > Links tagged with 'secondary protein structure'

Links tagged with 'secondary protein structure'

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Found 85 links

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3D-JuryTool Content

http://meta.bioinfo.pl/submit_wizard.pl [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.

links directory index: 775
TitlePublication YearGoogle Scholar Citation Count
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure2003115
3D-Jury: a simple approach to improve protein structure predictions2003592
Detection of reliable and unexpected protein fold predictions using 3D-Jury200368
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence homology computer simulation database management systems humans molecular models protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment tertiary protein structure

3D-pssmTool Content

http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html [open in a new window]

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Protein > 3-D Structure Prediction

Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.

links directory index: 1748
TitlePublication YearGoogle Scholar Citation Count
Enhanced genome annotation using structural profiles in the program 3D-PSSM20001568
CAFASP-1: critical assessment of fully automated structure prediction methods1999180
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome bacterial proteins computational biology factual databases flavoproteins integrases molecular models molecular sequence data mycoplasma open reading frames protein folding proteins proteome reproducibility of results retroviridae proteins ribonuclease h secondary protein structure sequence alignment solvents structure-activity relationship

AD-ENMTool Content

http://enm.lobos.nih.gov [open in a new window]

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Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Molecular Dynamics and Docking

Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.

links directory index: 256
TitlePublication YearGoogle Scholar Citation Count
Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin200545
Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved200552
Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model200559
A comparative study of motor-protein motions by using a simple elastic-network model2003100
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tagsactins adenosine triphosphate animals binding sites biophysical phenomena biophysics dictyostelium dna polymerase beta dna-directed rna polymerases elasticity humans kinesin ligands mice molecular conformation molecular models molecular motor proteins myosins nucleotides principal component analysis protein binding protein conformation proton-translocating atpases protozoan proteins secondary protein structure statistical models structure-activity relationship taq polymerase tertiary protein structure theoretical models thermodynamics viral proteins x-ray crystallography

AlphaPredTool Content

http://www.imtech.res.in/raghava/alphapred/ [open in a new window]

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Protein > 2-D Structure Prediction

The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.

This content is being maintained by raghavagps.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information200439
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tagsalpha-turns amino acid sequence ANN molecular sequence data neural networks (computer) prediction protein databases protein sequence analysis proteins roc curve secondary protein structure sequence alignment sequence-to-structure network statistical models structure-to-structure network

Ar_NHPredTool Content

http://www.imtech.res.in/raghava/ar_nhpred [open in a new window]

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Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes
Protein > Sequence Features

The Ar_NHPred server predicts the aromatic backbone NH interaction in a given amino acid sequence where the pi ring of aromatic residues interact with the backbone NH groups.

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links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
Role of evolutionary information in prediction of aromatic-backbone NH interactions in proteins20044
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tagsaromatic amino acids aromatic-backbone hydrogen bonding molecular evolution molecular models multiple sequence alignment Neural Network neural networks (computer) NH interactions protein protein databases proteins secondary protein structure sequence alignment sequence-to-structure network structure-to-structure network

BetatPred2Tool Content

http://www.imtech.res.in/raghava/betatpred2/ [open in a new window]

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Protein > 2-D Structure Prediction

The aim of BetaTPred2 server is to predict ß turns in proteins from multiple alignment by using neural network from the given amino acid sequence. For ß turn prediction, it uses the position specific score matrices generated by PSI-BLAST and secondary structure predicted by PSIPRED.

This content is being maintained by raghavagps.

links directory index: 94
TitlePublication YearGoogle Scholar Citation Count
Prediction of beta-turns in proteins from multiple alignment using neural network200394
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tagsalgorithms amino acid sequence beta-turns computer simulation factual databases molecular sequence data multiple sequence alignment neural networks (computer) prediction protein secondary protein structure statistical models

BhairPredTool Content

http://www.imtech.res.in/raghava/bhairpred/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.

This content is being maintained by raghavagps.

links directory index: 45
TitlePublication YearGoogle Scholar Citation Count
BhairPred: prediction of beta-hairpins in a protein from multiple alignment information using ANN and SVM techniques200545
NAR Web Server Issue 2005
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tagsalgorithms artificial intelligence neural networks (computer) protein sequence analysis secondary protein structure sequence alignment

BioInfo3DTool Content

http://bioinfo3d.cs.tau.ac.il/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Molecular Dynamics and Docking
Protein > Networks & Interactions, Pathways and Enzymes

BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.

This content is being maintained by BioInfo3D.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
BioInfo3D: a suite of tools for structural bioinformatics200424
NAR Web Server Issue 2004
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tagsalgorithms computational biology ligands macromolecular substances protein conformation proteins secondary protein structure

BOMPTool Content

http://www.bioinfo.no/tools/bomp [open in a new window]

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Protein > 2-D Structure Prediction
Protein > Localization and Targeting

The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.

links directory index: 85
TitlePublication YearGoogle Scholar Citation Count
BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria200485
NAR Web Server Issue 2004
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tagsbacterial genome bacterial outer membrane proteins escherichia coli gram-negative bacteria protein sequence analysis salmonella typhimurium secondary protein structure

BPROMPTTool Content

http://www.ddg-pharmfac.net/bprompt/BPROMPT/BPROMPT.html [open in a new window]

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Protein > 2-D Structure Prediction
Protein > Localization and Targeting

Bayesian PRediction Of Membrane Protein Topology (BPROMPT) uses a Bayesian Belief Network to combine the results of other membrane protein prediction methods for a protein sequence.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
BPROMPT: A consensus server for membrane protein prediction200337
NAR Web Server Issue 2003
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tagsbayes theorem eukaryotic cells membrane proteins prokaryotic cells protein sequence analysis reproducibility of results secondary protein structure

BSDBDatabase Content

http://www.ifpan.edu.pl/BSDB/ [open in a new window]

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Protein > Databases

The Biomolecule Stretching Data provides information about mechanostability of proteins. Its core is based on simulations of stretching of proteins within a structure-based model. The primary information is about the heights of the maximal force peaks, the force-displacement patterns, and the sequencing of the contact-rupturing events. Information on the possible types of the mechanical clamps (the motifs which are responsible for a protein's resistance to stretching) are also given.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
BSDB: the biomolecule stretching database20114
NAR Database Issue 2011
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tagsbiomechanics chemical models molecular dynamics simulation protein databases proteins secondary protein structure

BTEVALTool Content

http://www.imtech.res.in/raghava/bteval [open in a new window]

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The aim of BTEVAL server is to evaluate beta turn prediction algorithms on a uniform data set of 426 proteins or subsets of these proteins. It is the new data set in which no two protein chains have more that 25% sequence identity and each chain contains minimum one beta turn.

This content is being maintained by raghavagps.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
BTEVAL: a server for evaluation of beta-turn prediction methods20033
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tagsalgorithms amino acid sequence beta-turn btpred chou-fasman computational biology computer simulation gorbturn molecular models molecular sequence data prediction protein protein databases proteins secondary protein structure thornton

CATHDatabase Content

http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing

Database of automated protein structure classification according to Class (C), Architecture (A), Topology (T) and Homologous superfamily (H).

links directory index: 197
TitlePublication YearGoogle Scholar Citation Count
The CATH database: an extended protein family resource for structural and functional genomics2003197
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external linksLink on Wikipedia
tagsamino acid sequence homology animals automation genomics protein databases protein folding protein structural homology proteins secondary protein structure tertiary protein structure

CE-MCTool Content

http://bioinformatics.albany.edu/~cemc/ [open in a new window]

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Protein > 3-D Structure Comparison
Sequence Comparison > Multiple Sequence Alignments

A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.

links directory index: 146
TitlePublication YearGoogle Scholar Citation Count
CE-MC: a multiple protein structure alignment server200481
A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization200165
NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence amino acid sequence homology aspartic acid endopeptidases factual databases molecular sequence data monte carlo method protein kinases proteins secondary protein structure sequence alignment software design

CHpredictTool Content

http://www.imtech.res.in/raghava/chpredict [open in a new window]

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Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes

The CHpredict server predict two types of interactions: C-H...O and C-H...π interactions. For C-H...O interaction, the server predicts the residues whose backbone Cα atoms are involved in interaction with backbone oxygen atoms and for C-H...π interactions, it predicts the residues whose backbone Cα atoms are involved in interaction with π ring system of side chain aromatic moieties.

This content is being maintained by raghavagps.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Prediction of C alpha-H...O and C alpha-H...pi interactions in proteins using recurrent neural network20063
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tagsalgorithms alpha H O amino acid sequence ANN C alpha H pi computer simulation hydrogen bonding hydrogen bonding interactions molecular models molecular sequence data neural networks (computer) protein databases protein sequence analysis proteins secondary protein structure weak interactions

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