> Tag > Links tagged with 'protein conformation'

Links tagged with 'protein conformation'

RSS Feed Compact View Sort by Links Directory Index
downloadList as XML List as JSON List as TSV List as CSV

Found 159 links

Displaying 15 links

Hide Resources (4)Hide Databases (29)Hide Tools (126)

GeNMRTool Content

http://www.genmr.ca [open in a new window]

Share This Link
Protein > 3-D Structure Prediction

Generate NMR structures (GeNMR) is a web server for generating 3D protein structures using input sequence data, NOE-based distance restraints or NMR chemical shifts. Output is a set of PDB coordinates for the input protein.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
GeNMR: a web server for rapid NMR-based protein structure determination200919
NAR Web Server Issue 2009
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms biomolecular nuclear magnetic resonance molecular models protein conformation protein databases reproducibility of results

GlyprotTool Content

http://www.glycosciences.de/modeling/glyprot/php/main.php [open in a new window]

Share This Link
Other Molecules > Carbohydrates
Protein > 3-D Structural Features

Glyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure.

This content is being maintained by luetteke.

links directory index: 62
TitlePublication YearGoogle Scholar Citation Count
GlyProt: in silico glycosylation of proteins200562
NAR Web Server Issue 2005
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagscomputational biology glycoproteins glycosylation humans molecular models protein conformation protein isoforms

HexServerTool Content

http://hexserver.loria.fr/ [open in a new window]

Share This Link
Protein > Molecular Dynamics and Docking

A FFT-based protein docking server powered by graphics processors, HexServer rapidly produces a ranked list of docking predictions for input PDB protein structures.

links directory index: 28
TitlePublication YearGoogle Scholar Citation Count
HexServer: an FFT-based protein docking server powered by graphics processors201028
NAR Web Server Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms binding sites multiprotein complexes protein conformation

HHpredTool Content

http://protevo.eb.tuebingen.mpg.de/hhpred [open in a new window]

Share This Link
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Sequence Comparison > Similarity Searching and Classification

Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.

links directory index: 539
TitlePublication YearGoogle Scholar Citation Count
The HHpred interactive server for protein homology detection and structure prediction2005539
NAR Web Server Issue 2005
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence homology bacterial proteins markov chains protein conformation protein databases protein sequence analysis sequence alignment transcription factors

ICGEBnet Protein ToolsTool Content

http://www.icgeb.org/protein/ [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

ICGEBnet Protein Tools is a resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) and/or depth (DPX) indexes in 3D models.

links directory index: 191
TitlePublication YearGoogle Scholar Citation Count
CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures20058
DPX: for the analysis of the protein core200339
CX, an algorithm that identifies protruding atoms in proteins200247
Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison200297
NAR Web Server Issue 2005
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms animals chemical models cluster analysis computational biology crystallography humans interferon alfa-2a molecular evolution molecular models molecular structure probability programming languages protein conformation protein databases protein folding protein interaction mapping proteins secondary protein structure sensitivity and specificity sequence homology serpins tertiary protein structure trypsin

IEDB-3DDatabase Content

http://www.iedb.org [open in a new window]

Share This Link
Protein > Databases

IEDB-3D is the 3D structural component of the Immune Epitope Database (IEDB). IEDB-3D catalogs B- and T-cell epitopes and Major Histocompatibility Complex (MHC) ligands for which 3D structures of complexes with antibodies, T-cell receptors or MHC molecules are available in the Protein Data Bank (PDB). Journal articles that are primary citations of PDB structures and that define immune epitopes are curated within IEDB along with accompanying functional assays and immunologically relevant information. For each curated structure, IEDB-3D provides calculated data on intermolecular contacts and interface areas and includes an application, EpitopeViewer, to visualize the structures. IEDB-3D is fully embedded within IEDB, thus allowing structural data, both curated and calculated, and all accompanying information to be queried using multiple search interfaces. These include queries for epitopes recognized in different pathogens, eliciting different functional immune responses, and recognized by different components of the immune system.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
IEDB-3D: structural data within the immune epitope database20113
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsantibodies antigen receptors b-lymphocyte epitopes epitopes histocompatibility antigens ligands protein conformation protein databases t-lymphocyte epitopes

Institute of Enzymology ServersTool Content

http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=30&Itemid=... [open in a new window]

Share This Link
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting

A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.

links directory index: 2004
TitlePublication YearGoogle Scholar Citation Count
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates200546
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content2005392
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins2005235
BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes200552
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank2005138
Transmembrane proteins in the Protein Data Bank: identification and classification2004138
Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation200443
SCide: identification of stabilization centers in proteins.20030
Servers for sequence-structure relationship analysis and prediction20035
On filtering false positive transmembrane protein predictions200257
The HMMTOP transmembrane topology prediction server.20010
Principles governing amino acid composition of integral membrane proteins: application to topology prediction1998795
Stabilization centers in proteins: identification, characterization and predictions1997103
NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence amino acids binding sites capsid proteins cell line chemical models computational biology computer simulation conserved sequence cysteine database management systems dna methylation dna primers drug stability energy transfer genome genomics humans hydrophobic and hydrophilic interactions kringles lipid bilayers markov chains membrane proteins molecular models molecular sequence data neural networks (computer) oxidation-reduction pliability polymerase chain reaction protein binding protein conformation protein databases protein engineering protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment statistical models structure-activity relationship sulfites temperature tertiary protein structure thermodynamics tissue plasminogen activator

IntFOLDTool Content

http://www.reading.ac.uk/bioinf/IntFOLD/ [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

The IntFOLD web server is an integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction20119
NAR Web Server Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsbinding sites ligands molecular models protein conformation protein folding protein sequence analysis tertiary protein structure

INTREPIDTool Content

http://phylogenomics.berkeley.edu/intrepid [open in a new window]

Share This Link
Protein > Annotation and Function
Protein > Sequence Features

The INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures if available.

This content is being maintained by kimmen.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis200911
NAR Web Server Issue 2009
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence homology amino acids catalytic domain molecular models phylogeny protein conformation protein sequence analysis proteins

iPBATool Content

http://www.dsimb.inserm.fr/dsimb_tools/ipba/ [open in a new window]

Share This Link
Protein > 3-D Structure Comparison

iPBA uses specialized protein block substitution matrices and anchor based methodology for pairwise protein structure comparisons.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
iPBA: a tool for protein structure comparison using sequence alignment strategies20113
NAR Web Server Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms protein conformation protein databases protein sequence analysis sequence alignment

JEvTraceTool Content

http://www.cmpharm.ucsf.edu/~marcinj/JEvTrace/ [open in a new window]

Share This Link
Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins.

links directory index: 845
TitlePublication YearGoogle Scholar Citation Count
JEvTrace: refinement and variations of the evolutionary trace in JAVA200218
An evolutionary trace method defines binding surfaces common to protein families1996827
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence amino acid sequence homology animals bacterial proteins binding sites carrier proteins conserved sequence dna-binding proteins factual databases genetic variation glucocorticoid receptors haemophilus influenzae humans molecular evolution molecular models molecular sequence data mutation phylogeny protein conformation proteins quaternary protein structure rats rna-binding proteins sequence alignment src homology domains streptococcus pneumoniae zinc fingers

KFC ServerTool Content

http://www.mitchell-lab.org/kfc [open in a new window]

Share This Link
Protein > 3-D Structural Features

The KFC Server is a web-based implementation of the Knowledge-based FADE and Contacts (KFC) model. KFC predicts the subset of residues responsible for the majority of a protein interface's binding free energy. Users input protein-protein or protein-DNA information for visualization of binding hot spots within the protein structure.

links directory index: 29
TitlePublication YearGoogle Scholar Citation Count
KFC Server: interactive forecasting of protein interaction hot spots200829
NAR Web Server Issue 2008
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsartificial intelligence binding sites molecular models multiprotein complexes protein conformation protein interaction mapping

KINARI-WebTool Content

http://kinari.cs.umass.edu/ [open in a new window]

Share This Link
Protein > 3-D Structural Features

KINARI-Web is a web server for performing rigidity analysis and visually exploring rigidity properties of proteins. It also provides tools for pre-processing the input data, such as selecting relevant chains from PDB files, adding hydrogen atoms and identifying stabilizing interactions.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
KINARI-Web: a server for protein rigidity analysis20118
NAR Web Server Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsligands molecular models protein conformation

KinDOCKTool Content

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

Share This Link
Protein > 3-D Structural Features
Protein > Molecular Dynamics and Docking

KinDOCK is a tool for the analysis of ATP-binding sites of protein kinases based on a structural library of protein kinase-ligand complexes extracted from the Protein Data Bank (PDB).

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
kinDOCK: a tool for comparative docking of protein kinase ligands200611
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsadenosine triphosphate binding sites drug design ligands protein conformation protein kinase inhibitors protein kinases

KNOTSTool Content

http://knots.mit.edu/ [open in a new window]

Share This Link
Protein > 3-D Structural Features

KNOTS is a web server that detects knots in protein structures.

This content is being maintained by virnau.

links directory index: 127
TitlePublication YearGoogle Scholar Citation Count
Protein knot server: detection of knots in protein structures200731
Intricate knots in proteins: Function and evolution200696
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms bacterial proteins computational biology computer simulation cysteine endopeptidases genetic databases haemophilus influenzae humans molecular evolution molecular models protein binding protein conformation protein databases protein folding proteins statistical models tertiary protein structure

Associated Tag Cloud