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Links tagged with 'solvents'

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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

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

FOLD-RATETool Content

http://psfs.cbrc.jp/fold-rate/ [open in a new window]

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Protein > Molecular Dynamics and Docking

FOLD-RATE predicts the folding rates of proteins from their amino acid sequences.

links directory index: 353
TitlePublication YearGoogle Scholar Citation Count
FOLD-RATE: prediction of protein folding rates from amino acid sequence200676
A statistical model for predicting protein folding rates from amino acid sequence with structural class information200549
Importance of native-state topology for determining the folding rate of two-state proteins200331
Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction2001197
NAR Web Server Issue 2006
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tagsamino acid sequence amino acids binding sites chemical models kinetics linear models molecular models mutation protein conformation protein folding protein sequence analysis protein structural homology proteins secondary protein structure solvents statistical models statistics as topic tertiary protein structure thermodynamics

NORSpTool Content

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

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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
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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

PDB2PQR ServerTool Content

http://pdb2pqr.sourceforge.net/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features

Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures.

links directory index: 581
TitlePublication YearGoogle Scholar Citation Count
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations2007151
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations2004430
NAR Web Server Issue 2004NAR Web Server Issue 2007
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tagscomputational biology computer simulation hydrogen hydrogen bonding ligands mathematical computing molecular conformation molecular structure programming languages protein databases proteins solvents static electricity

PDB_HydroTool Content

http://lorentz.immstr.pasteur.fr/solvate_mutate.php [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features

PDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones.

This content is being maintained by Marc Delarue.

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics200627
NAR Web Server Issue 2006
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tagsbinding sites dimerization lipids mathematical computing membrane proteins nucleic acids protein conformation protein databases proteins solvents static electricity water

PI2PETool Content

http://pipe.scs.fsu.edu/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes

PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.

links directory index: 473
TitlePublication YearGoogle Scholar Citation Count
PI2PE: protein interface/interior prediction engine200718
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces200751
Prediction of solvent accessibility and sites of deleterious mutations from protein sequence200549
Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data2005111
Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading200136
Prediction of protein interaction sites from sequence profile and residue neighbor list2001208
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids animals artificial intelligence binding sites biomolecular nuclear magnetic resonance computational biology computer simulation dna dna-binding proteins factual databases genomic library hydrophobic and hydrophilic interactions membrane proteins molecular conformation molecular models molecular sequence data mutation mycoplasma neural networks (computer) open reading frames prions protein binding protein conformation protein sequence analysis proteins quaternary protein structure reproducibility of results rna-binding proteins saccharomyces cerevisiae secondary protein structure sequence alignment solvents

POPSTool Content

http://mathbio.nimr.mrc.ac.uk/wiki/POPS [open in a new window]

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Protein > 3-D Structural Features

Parameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level.

links directory index: 114
TitlePublication YearGoogle Scholar Citation Count
POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level200349
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome200265
NAR Web Server Issue 2003
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tagsalgorithms amino acids hydrophobic and hydrophilic interactions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein binding protein conformation proteins ribosomal proteins ribosomal rna ribosomes solvents time factors transfer rna

RPBSResource Content

http://bioserv.rpbs.jussieu.fr/ [open in a new window]

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Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Biochemical Features
Protein > Sequence Features

Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP).

This content is being maintained by jompo.

links directory index: 852
TitlePublication YearGoogle Scholar Citation Count
RPBS: a web resource for structural bioinformatics200520
Filtering redundancies for sequence similarity search programs20053
Local backbone structure prediction of proteins200443
New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification1999103
PredAcc: prediction of solvent accessibility199945
A global taxonomy of loops in globular proteins199684
Automat and BLAST: comparison of two protein sequence similarity search programs19952
Automat: a novel software system for the systematic search for protein (or DNA) similarities with a notable application to autoimmune diseases and AIDS19948
Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences1987544
NAR Web Server Issue 2005
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tagsacquired immunodeficiency syndrome algorithms amino acid sequence amino acid sequence homology amino acids animals arabidopsis autoimmune diseases azurin bacterial genome chemical models computational biology computer simulation computer-assisted numerical analysis consensus sequence database management systems dna dna sequence analysis evaluation studies as topic factual databases genetic databases globins glycine hiv humans hydrolases leghemoglobin logistic models methods molecular models molecular sequence data nucleic acid sequence homology plant genome plastocyanin protein conformation protein structural homology proteins rats reproducibility of results secondary protein structure sequence alignment sequence analysis sequence homology solvents thiosulfate sulfurtransferase

SARpredTool Content

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

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Protein > 2-D Structure Prediction
Sequence Comparison > Multiple Sequence Alignments

SARpred, a neural network based method predicts the real value of surface acessibility by using multiple sequence alignment.

This content is being maintained by raghavagps.

links directory index: 50
TitlePublication YearGoogle Scholar Citation Count
Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure200550
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tagsamino acids neural networks neural networks (computer) prediction protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence-to-structure network solvent accessibility solvents structure-to-structure network surface accessibility thioredoxins

SCRATCHTool Content

http://www.igb.uci.edu/servers/psss.html [open in a new window]

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

SCRATCH is a suite of protein structure software and servers for the prediction of secondary structure, solvent accessibility, disulphide bridges, stability effects of single amino acid mutations, disordered regions, domains, beta-residue and beta-strand pairings, amino acid contact maps, and tertiary structure.

links directory index: 295
TitlePublication YearGoogle Scholar Citation Count
SCRATCH: a protein structure and structural feature prediction server2005295
NAR Web Server Issue 2005
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tagsdisulfides mutation protein conformation proteins secondary protein structure solvents tertiary protein structure

SPACETool Content

http://ligin.weizmann.ac.il/space/ [open in a new window]

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Protein > 3-D Structure Prediction

SPACE (Structure Prediction and Analysis based on Complementarity with Environment) is a suite of tools for predicting and analyzing structures of biomolecules and their complexes.

This content is being maintained by lpsobol.

links directory index: 692
TitlePublication YearGoogle Scholar Citation Count
SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment200537
Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins200456
MutaProt: a web interface for structural analysis of point mutations20019
Automated analysis of interatomic contacts in proteins1999457
Molecular docking using surface complementarity1996133
NAR Web Server Issue 2005
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tagsalgorithms amino acids automation bacterial proteins binding sites biotin computational biology factual databases formycins hydrogen bonding ligands molecular conformation molecular models molecular structure nucleic acids point mutation protein binding protein conformation protein databases proteins ribonucleotides ricin site-directed mutagenesis solvents streptavidin thermodynamics water x-ray crystallography

TBBpredTool Content

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

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Protein > Sequence Features

Transmembrane Beta Barrel prediction server predicts the transmembrane Beta barrel regions in a given protein sequence. The server uses a forked strategy for predicting residues which are in transmembrane beta barrel regions. Prediction can be done based only on neural networks or based on statistical learning technique - SVM or combination of two methods.

This content is being maintained by raghavagps.

links directory index: 75
TitlePublication YearGoogle Scholar Citation Count
Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods200475
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tagsalgorithms ANN bacterial proteins beta-barrel cell membrane computational biology computer simulation hydrophobic and hydrophilic interactions machine learning techniques membrane proteins molecular evolution molecular models neural networks (computer) pliability secondary protein structure sensitivity and specificity sequence alignment solvents SVM thermodynamics transmembrane

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