> Tag > Links tagged with 'structure-activity relationship'

Links tagged with 'structure-activity relationship'

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

Found 27 links

Displaying 15 links

Resources (0)Hide Databases (4)Hide Tools (23)

3D-pssmTool Content

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

Share This Link
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
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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]

Share This Link
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
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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

Bimas HLA Peptide Binding PredictionsDatabase Content

http://www-bimas.cit.nih.gov/molbio/hla_bind/ [open in a new window]

Share This Link
Protein > Databases

Function: Rank potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules. The analysis is based on coefficient tables deduced from the published literature.

links directory index: 1187
TitlePublication YearGoogle Scholar Citation Count
Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains19941187
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence antigens beta 2-microglobulin chemical models competitive binding hla-a2 antigen immunogenicity prediction molecular sequence data oligopeptides protein binding structure-activity relationship

BioBayesNetTool Content

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

Share This Link
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
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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

ChemMine ToolsTool Content

http://chemmine.ucr.edu [open in a new window]

Share This Link
Other Molecules > Small Molecules

ChemMine Tools is an online service for analyzing and clustering small molecules. A suite of cheminformatics and data mining tools for data visualization, structure comparison, similarity searching, compound clustering and prediction of chemical properties are available.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ChemMine tools: an online service for analyzing and clustering small molecules20116
NAR Web Server Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms cluster analysis data mining drug discovery genomics pharmaceutical preparations small molecule libraries structure-activity relationship

DiANNATool Content

http://bioinformatics.bc.edu/clotelab/DiANNA/ [open in a new window]

Share This Link
Protein > Biochemical Features
Protein > Sequence Features

DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.

links directory index: 89
TitlePublication YearGoogle Scholar Citation Count
DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification200625
DiANNA: a web server for disulfide connectivity prediction200564
Disulfide connectivity prediction using secondary structure information and diresidue frequencies.20050
NAR Web Server Issue 2005NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms artificial intelligence binding sites chemical models computer simulation cysteine disulfides neural networks (computer) oxidation-reduction protein binding protein conformation protein interaction mapping protein sequence analysis proteins secondary protein structure sequence alignment structure-activity relationship

DINAMeltTool Content

http://mfold.rna.albany.edu/?q=DINAMelt [open in a new window]

Share This Link
DNA > Tools For the Bench
RNA > Structure Prediction, Visualization, and Design

DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.

links directory index: 944
TitlePublication YearGoogle Scholar Citation Count
DINAMelt web server for nucleic acid melting prediction2005378
Prediction of hybridization and melting for double-stranded nucleic acids2004129
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding1994437
NAR Web Server Issue 2005
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms animals bacterial rna base sequence calorimetry dna dna sequence analysis fungal rna genetic hybridization introns molecular sequence data nucleic acid conformation nucleic acid denaturation nucleic acid hybridization oligonucleotides oligoribonucleotides phylogeny rats rna rna sequence analysis single-stranded dna structure-activity relationship temperature theoretical models transition temperature

eF-seekTool Content

http://ef-site.hgc.jp/eF-seek/index.jsp [open in a new window]

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

eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.

This content is being maintained by Kenta Nakai.

links directory index: 409
TitlePublication YearGoogle Scholar Citation Count
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape200727
Identification of the ligand binding sites on the molecular surface of proteins200547
eF-site and PDBjViewer: database and viewer for protein functional sites200472
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site2003118
Protein informatics towards function identification200352
Identification of protein functions from a molecular surface database, eF-site200293
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms antibodies binding sites biological models computational biology computer simulation database management systems ligands molecular models protein conformation protein databases protein folding proteins proteomics s-adenosylhomocysteine static electricity structure-activity relationship three-dimensional imaging trypsin

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

MarkUsTool Content

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Mark-Us [open in a new window]

Share This Link
Protein > 3-D Structure Comparison
Protein > Annotation and Function

MarkUs is a web server for analysis and comparison of the structural and functional properties of proteins.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
MarkUs: a server to navigate sequence-structure-function space.20111
NAR Web Server Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsbacterial proteins protein conformation proteins structure-activity relationship

MutDBDatabase Content

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

Share This Link
DNA > Annotations
DNA > Sequence Polymorphisms

MutDB is a database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
MutDB services: interactive structural analysis of mutation data200533
MutDB: annotating human variation with functionally relevant data200331
NAR Web Server Issue 2005
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid substitution database management systems documentation genetic databases genetic predisposition to disease genetic variation human genome humans molecular models mutation phenotype protein conformation protein databases protein sequence analysis proteins sequence alignment single nucleotide polymorphism structure-activity relationship

NORSpTool Content

http://cubic.bioc.columbia.edu/services/NORSp/ [open in a new window]

Share This Link
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.

links directory index: 251
TitlePublication YearGoogle Scholar Citation Count
NORSp: Predictions of long regions without regular secondary structure2003106
Loopy proteins appear conserved in evolution2002145
NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acids computational biology conserved sequence genetic transcription hydrogen bonding molecular evolution molecular models pliability protein binding protein databases protein folding protein sequence analysis proteins proteome secondary protein structure software design solvents structure-activity relationship

oGNMTool Content

http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm [open in a new window]

Share This Link
Protein > Molecular Dynamics and Docking

Online Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.

links directory index: 795
TitlePublication YearGoogle Scholar Citation Count
oGNM: online computation of structural dynamics using the Gaussian Network Model200651
iGNM: a database of protein functional motions based on Gaussian Network Model200587
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential1997657
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms binding sites chemical models computational biology computer simulation molecular models molecular structure motion normal distribution nucleic acid conformation oligonucleotides protein binding protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship thermodynamics x-ray crystallography

ProtTestTool Content

http://darwin.uvigo.es/software/prottest_server.html [open in a new window]

Share This Link
Protein > Phylogeny Reconstruction

ProtTest is a program that determines the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment.

links directory index: 1077
TitlePublication YearGoogle Scholar Citation Count
ProtTest: selection of best-fit models of protein evolution20051077
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence amino acid substitution amino acids computer simulation dna mutational analysis genetic models humans molecular evolution molecular models molecular sequence data phylogeny protein sequence analysis proteins site-directed mutagenesis structure-activity relationship

pTARGETTool Content

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

Share This Link
Protein > Localization and Targeting

pTARGET predicts the subcellular localization of eukaryotic proteins based on the occurrence patterns of location-specific protein functional domains and the amino acid compositional differences in proteins from nine distinct subcellular locations.

links directory index: 40
TitlePublication YearGoogle Scholar Citation Count
pTARGET: a web server for predicting protein subcellular localization200640
pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes.20050
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence animals eukaryotic cells humans mice molecular sequence data protein sequence analysis proteins proteome proteomics sequence alignment structure-activity relationship subcellular fractions

Associated Tag Cloud