> Tag > Links tagged with 'protein folding'

Links tagged with 'protein folding'

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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

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

links directory index: 98
TitlePublication YearGoogle Scholar Citation Count
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures20073
Query3d: a new method for high-throughput analysis of functional residues in protein structures200536
A structural study for the optimisation of functional motifs encoded in protein sequences20047
Three-dimensional profiles: a new tool to identify protein surface similarities199852
NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/ [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes200914
NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

links directory index: 627
TitlePublication YearGoogle Scholar Citation Count
Tools for comparative protein structure modeling and analysis2003190
Modeller: generation and refinement of homology-based protein structure models2003437
NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

BioBayesNetTool Content

http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Sequence Features

BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.

links directory index: 33
TitlePublication YearGoogle Scholar Citation Count
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data20078
A multiple-feature framework for modelling and predicting transcription factor binding sites200525
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence automated pattern recognition bayes theorem binding sites chemical models computational biology computer simulation dna sequence analysis genetic models molecular models molecular sequence data protein binding protein conformation protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship transcription factors

Cascade PSI-BlastDatabase Content

http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html [open in a new window]

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Protein > Domains and Motifs
Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching and Classification

Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains20068
Assessment of a rigorous transitive profile based search method to detect remotely similar proteins200510
NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology molecular models molecular sequence data protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment tertiary protein structure

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

CATHDatabase Content

http://www.cathdb.info/ [open in a new window]

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Protein > Databases

CATH is a manually curated classification of protein domain structures. Each protein has been chopped into structural domains and assigned into homologous superfamilies (groups of domains that are related by evolution). This classification procedure uses a combination of automated and manual techniques which include computational algorithms, empirical and statistical evidence, literature review and expert analysis.

links directory index: 20
TitlePublication YearGoogle Scholar Citation Count
Extending CATH: increasing coverage of the protein structure universe and linking structure with function201120
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsphylogeny protein databases protein folding proteins tertiary protein structure

Combinatorial Extension of the Optimal PathDatabase Content

http://cl.sdsc.edu/ce.html [open in a new window]

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Protein > 3-D Structure Comparison

Calculates structural alignments between two protein chains; or between a single chain and the entire Protein Data Bank.

links directory index: 1542
TitlePublication YearGoogle Scholar Citation Count
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path19981542
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tagsalgorithms amino acid sequence amino acid sequence homology molecular sequence data monte carlo method protein conformation protein folding proteins sequence alignment

COPSTool Content

http://cops.services.came.sbg.ac.at/ [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
COPS--a novel workbench for explorations in fold space200914
NAR Web Server Issue 2009
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tagsmolecular models protein databases protein folding proteins tertiary protein structure

CPHmodels-3.0Tool Content

http://www.cbs.dtu.dk/services/CPHmodels/ [open in a new window]

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Protein > 3-D Structure Prediction

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles201037
NAR Web Server Issue 2010
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tagsalgorithms protein folding protein sequence analysis protein structural homology reproducibility of results

CUPSATTool Content

http://cupsat.uni-koeln.de/ [open in a new window]

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Protein > 3-D Structure Prediction
Protein > Biochemical Features

Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures.

links directory index: 95
TitlePublication YearGoogle Scholar Citation Count
CUPSAT: prediction of protein stability upon point mutations200695
NAR Web Server Issue 2006
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tagsmolecular structure point mutation protein databases protein denaturation protein engineering protein folding proteins secondary protein structure solvents

DBCPTool Content

http://120.107.8.16/dbcp [open in a new window]

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

The Disulfide Bonding Connectivity Pattern (DBCP) web server tool provides prediction of disulphide bonding connectivity patterns without the prior knowledge of the bonding states of cysteines. Useful in locating disulphide bridges and helping to solve protein folding.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
DBCP: a web server for disulfide bonding connectivity pattern prediction without the prior knowledge of the bonding state of cysteines20107
NAR Web Server Issue 2010
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tagscysteine disulfides protein conformation protein folding protein sequence analysis proteins reproducibility of results

DOMACTool Content

http://casp.rnet.missouri.edu/domac.html [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching and Classification

DOMAC is an accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together.

links directory index: 156
TitlePublication YearGoogle Scholar Citation Count
DOMAC: an accurate, hybrid protein domain prediction server200731
A machine learning information retrieval approach to protein fold recognition2006125
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology animals artificial intelligence computational biology genetic databases humans molecular models molecular sequence data normal distribution protein databases protein folding protein sequence analysis proteins secondary protein structure sensitivity and specificity sequence alignment statistical models tertiary protein structure

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