> Tag > Links tagged with 'hydrogen bonding'

Links tagged with 'hydrogen bonding'

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Found 15 links

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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.

This content is being maintained by raghavagps.

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

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

DSSPcontTool Content

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

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Protein > 2-D Structure Prediction

DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.

links directory index: 60
TitlePublication YearGoogle Scholar Citation Count
DSSPcont: Continuous secondary structure assignments for proteins200360
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence biomolecular nuclear magnetic resonance hydrogen bonding molecular models proteins secondary protein structure

MolProbityTool Content

http://molprobity.biochem.duke.edu/ [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
RNA > Structure Prediction, Visualization, and Design

MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculates global and local validation for all-atom contacts (steric clashes, H-bonds & vdW), covalent geometry, and conformation (Ramachandran & rotamers for protein, ribose puckers & suite conformers for RNA). Results are displayed online as 3D graphics and sortable charts.

This content is being maintained by dcrjsr.

links directory index: 2881
TitlePublication YearGoogle Scholar Citation Count
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids20071156
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes2004401
Structure validation by Calpha geometry: phi,psi and Cbeta deviation20031324
NAR Web Server Issue 2004NAR Web Server Issue 2007
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tagscomputational biology hydrogen bonding hydrogens molecular graphics molecular models molecular structure nucleic acid conformation protein protein conformation reproducibility of results rna structure validation three-dimensional imaging

MoViESTool Content

http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl [open in a new window]

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DNA > Structure and Sequence Feature Detection
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking
RNA > Structure Prediction, Visualization, and Design

MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. Analysis of vibrational motions and thermal fluctuational dynamics can give insights into the functional properties of both proteins and nucleic acids.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids200415
NAR Web Server Issue 2004
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tagscomputational biology hydrogen bonding nucleic acids proteins thermodynamics vibration

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

NRSASTool Content

http://www.receptors.org/NR/servers/html/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features

Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
NRSAS: Nuclear Receptor Structure Analysis Servers20032
NAR Web Server Issue 2003
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tagscytoplasmic and nuclear receptors hormones hydrogen bonding molecular models mutation protein conformation protein structural homology

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

PICTool Content

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

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

Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex.

links directory index: 88
TitlePublication YearGoogle Scholar Citation Count
PIC: Protein Interactions Calculator200788
NAR Web Server Issue 2007
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tagsamino acids animals computational biology humans hydrogen bonding molecular conformation molecular models molecular structure plant proteins protein databases proteins

pKD ServerTool Content

http://enzyme.ucd.ie/cgi-bin/pKD/server_start.cgi [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features

pKa Design (pKD) takes as input a protein structure and allows you to redesign the protein pKa value for that molecule. The server calculates a set of point mutations that will cause the desired pKa change.

links directory index: 178
TitlePublication YearGoogle Scholar Citation Count
pKD: re-designing protein pKa values200622
Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations2001156
NAR Web Server Issue 2006
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tagsamino acid sequence hydrogen bonding hydrogen-ion concentration mathematics molecular models point mutation protein conformation proteins static electricity x-ray crystallography

ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > 3-D Structural Features

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

links directory index: 318
TitlePublication YearGoogle Scholar Citation Count
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition200628
Intermolecular and intramolecular readout mechanisms in protein-DNA recognition200487
Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding200262
Structure-based prediction of DNA target sites by regulatory proteins1999141
NAR Web Server Issue 2006
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tagsbacterial proteins base sequence binding sites biological models dimerization dna dna primers dna-binding proteins endonucleases gene expression regulation genetic promoter regions glucocorticoid receptors hydrogen bonding macromolecular substances metalloproteins molecular models nucleic acid conformation protein binding protein conformation protein kinases protein subunits proteins repressor proteins saccharomyces cerevisiae proteins tertiary protein structure thermodynamics type ii site-specific deoxyribonucleases viral proteins viral regulatory and accessory proteins water zinc fingers

Services from Zhou LaboratoryResource Content

http://cssb.biology.gatech.edu/skolnick/people/zhou.html [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Networks & Interactions, Pathways and Enzymes

Tools from the Zhou laboratory including predictors of transmembrane topology (THUMBUP, UMDHMM-TMHP, TUPS); prediction/analysis tools for tertiary structure (SPARKS2, SP3); and, prediction/analysis tools for interactions (DMONOMER, DLOOP, DMUTANT, DCOMPLEX, DDNA, TCD, DOGMA).

links directory index: 1058
TitlePublication YearGoogle Scholar Citation Count
Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations200520
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments2005136
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential200473
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition2004135
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding200492
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method200360
Folding rate prediction using total contact distance2002139
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction2002403
NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids antigen-antibody complex binding sites biological evolution chemical models computational biology dimerization factual databases hydrogen bonding kinetics markov chains mathematics membrane proteins molecular evolution molecular structure peptide fragments peptide library plant proteins probability protein binding protein conformation protein databases protein folding protein sequence analysis proteins regression analysis reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical models statistics as topic tertiary protein structure theoretical models thermodynamics time factors

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

STING MilleniumTool Content

http://luna.bioc.columbia.edu/SMS/STINGm/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

links directory index: 168
TitlePublication YearGoogle Scholar Citation Count
The Diamond STING server200522
STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database200516
STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces200415
Defining 3D residue environment in protein structures using SCORPION and FORMIGA20043
ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure200415
STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes200422
JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure200422
STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence200344
Analysis of structural and physico-chemical parameters involved in the specificity of binding between alpha-amylases and their inhibitors20009
NAR Web Server Issue 2003NAR Web Server Issue 2005
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tagsacid anhydride hydrolases algorithms alpha-amylases amino acid sequence amino acid sequence homology amino acids animals beetles binding sites chemical models chymotrypsin color computational biology computer simulation conserved sequence enzyme inhibitors fabaceae hiv integrase hydrogen bonding lectins medicinal plants molecular cloning molecular models molecular sequence data molecular structure online systems ovomucin plant lectins plant proteins proprotein convertases protein binding protein conformation protein databases protein interaction mapping protein sequence analysis protein structural homology proteins quaternary protein structure recombinant proteins sequence alignment structure-activity relationship systems integration x-ray crystallography

VADARTool Content

http://redpoll.pharmacy.ualberta.ca/vadar/ [open in a new window]

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

Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data.

links directory index: 189
TitlePublication YearGoogle Scholar Citation Count
VADAR: a web server for quantitative evaluation of protein structure quality2003189
NAR Web Server Issue 2003
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tagsalgorithms hydrogen bonding molecular structure protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure

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