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Links tagged with 'hydrogen bonding'

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DSSPcontTool Content

http://cubic.bioc.columbia.edu/services/DSSPcont/

Protein > 2-D Structure Prediction

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

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

FastContactTool Content

http://structure.pitt.edu/servers/fastcontact/

Protein > Molecular Dynamics and Docking

FastContact is a free energy scoring tool for protein-protein complex structures.

NAR Web Server Issue 2007
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tagsalgorithms amino acids binding sites biological models chemical models computational biology computer simulation hydrogen bonding molecular models protein binding protein conformation protein interaction mapping protein sequence analysis proteins solvents static electricity thermodynamics

HarmonyTool Content

http://caps.ncbs.res.in/harmony/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Sequence Comparison > Analysis of Aligned Sequences

Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.

NAR Web Server Issue 2006
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tagsalgorithms amino acid substitution amino acids hydrogen bonding molecular models protein conformation protein sequence analysis proteins solvents

JOYTool Content

http://tardis.nibio.go.jp/cgi-bin/joy/joy.cgi

Protein > 3-D Structure Retrieval/Viewing
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization

JOY is a program for displaying 3D structural information in a multiple sequence alignment.

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tagsamino acid sequence hydrogen bonding molecular sequence data protein conformation proteins secondary protein structure sequence alignment

MolProbityTool Content

http://molprobity.biochem.duke.edu/

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.

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

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.

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/

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.

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/

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.

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/

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.

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

PFPTool Content

http://pfp.technion.ac.il/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.

This content is being maintained by shulash3.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence binding sites computational biology dna-binding proteins hydrogen bonding hydrogen-ion concentration molecular conformation molecular models molecular sequence data neural networks (computer) plant proteins programming languages protein binding protein conformation protein databases proteins static electricity surface properties viral proteins

PICTool Content

http://crick.mbu.iisc.ernet.in/~PIC/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, 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.

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

ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/

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.

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

SPACETool Content

http://ligin.weizmann.ac.il/space/

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.

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/

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.

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

STRIDETool Content

http://webclu.bio.wzw.tum.de/stride/

Protein > 2-D Structure Prediction

STRIDE takes a PDB structure as input and reports back either secondary structure assignments, a Ramachandran plot or a contact map.

NAR Web Server Issue 2004
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tagshydrogen bonding molecular structure protein databases proteins secondary protein structure