Tuesday, February 10, 2009

An excellent site to aid Protein Structural Analysis

Our Group Resources listed:

PALI - Phylogeny and ALIgnment of homologous protein structures.
SUPFAM - Clusters of potentially related homologous protein domain families.

More Resources


CCP4 Molecular Graphics - Create beautiful publication quality images and movies.
Chimera - Interactive visualization and analysis of molecular structures and related data.
COOT - Main website for model-building/visualization program; COOT Manual
GRASP2 - Macromolecular structure and surface visualization written for the Windows.
LigPlot - Automatically plots protein-ligand interactions.
PYMOL - A molecular visualization system on an OPEN-SOURCE foundation. Wiki  Mailing-list
Raster3D - Program suite for photo-realistic molecular graphics.
SwissPDB Viewer - Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly
interface allowing to analyze several proteins at the same time
.  Tutorial
TopDraw - Sketchpad for drawing topology cartoons of proteins.

Structural and Sequence Alignment

AL2CO - Takes the multiple alignment and maps the positional conservation in the B-factor column of
the structure.
Baton - Structure based sequence alignment output file in the JOY format.
CE Combinatorial Extension Method - 3-D Protein Structure Comparison and Alignment.
CEMC -  Multiple protein structure alignment server.
ClustalW2 - A general purpose multiple sequence alignment program for DNA or proteins.
DALI - A server for comparing protein structures in 3D.
DALI Lite - Pairwise comparison of protein structures.
ESPript - Utility to generate a attractive PostScript output from aligned sequences.
FPS -  A method for scoring a query sequence against a family of sequences.
Homolmapper - Map several conserved properties onto your structures, not just plain sequence.
Indonesia -  Integrated program package for biological sequence analysis.
MAMMOTH - Multiple protein structure alignment server.
Mustang - Multiple structural alignment algorithm.
PALI - Phylogeny and ALIgnment of homologous protein structures.
Rapido - Alignment of protein structures in the presence of conformational changes. REF
SSM - Secondary Structure Matching: a tool for protein structure comparison
Stralign - Structure alignment program.
STRAP - Structure based alignment program.
Structural Alignment of SCOP Sequences - search the results of structural comparisons.
SUPFAM - Clusters of potentially related homologous protein domain families.
TCoffee - Evaluating multiple alignments of DNA, RNA, protein sequences and structures.
Theseus - Maximum likelihood superpositioning and analysis of macromolecular structures.
3D SS - Three dimensional structure superposition.

General Analysis

AMIGOS -  Reads an RNA PDB file and outputs a complete table of torsion angle calculations.
APBS - Software for evaluating the electrostatic properties of nanoscale biomolecular systems.
Atlas of Protein Side-Chain Interactions - depicts how amino acid side-chains pack.
CATH - Hierarchical classification of protein domain structures.
CAVENV - Designed to help visualise cavities in a protein structure.
CAVER - Automated calculation of pathways leading from buried cavities to outside solvent in static and
dynamic protein structures.
CaPTURE - Identify energetically significant cation-pi interactions within proteins.
CASTp - Computed atlas of surface topography of proteins.
ConSurf - Identification of Functional Regions in Proteins.
DDMP -- Differences Distance Matrix Program.
Dynamite - Makes predictions about the way a protein moves given only a PDB file.
Dynapocket - Prediction of likely configurations of the atoms of binding pocket.
DynDom - Determine domains, hinge axes and hinge bending residues in proteins.
dssp2pdb - Converts dssp output to pdb.
eF-site - Electrostatic surface of functional site.
elNemo - Compute the low frequency normal modes of a protein.
Entangle - Creates a listing of interactions that occur at the interface between the nucleic-acid/protein
complex. These interactions are then classified into hydrogen bonds, electrostatic, hydrophobic, and
Van der Waals.
ESCET - Analyse and compare three-dimensional protein structures.
extpdb - If you cut up pdb files, this is the utility for you.
FISH - Domain identification server.
GETAREA - Calculation of solvent accessible surface areas, atomic solvation energies and their
gradients for macromolecules.
GROMACS - Versatile package to perform molecular dynamics.
HBexplore - Geometrical analysis of hydrogen bonds in biological macromolecules.
InterPro - Database of protein families, domains, repeats and sites.
iMolTalk - Structural Bioinformatics Toolkit; an interactive, Internet-based service for computational
analyses in Structural Biology.
MOLEOline -  Web-based tool to find/analyze molecular channels, tunnels and pores.
MolProbity - An expert-system consultation about the accuracy of a macromolecular structure.
MOTIF - Sequence motif search from GenomeNet.
MSDMotif - Provides information about ligands, sequence and structure motifs.
NACCESS - Calculates the accessible area of a molecule from a PDB format file.
NCBI BLAST - Finds regions of similarity between biological sequences.
OCA - A browser-database for protein structure/function.
OnD-CRF - Order and Disorder in proteins prediction server.
Parvati -  Analysis/validation tool for high resolution protein structures.
PDBsum - At-a-glance overview of every macromolecular structure deposited in the PDB.
PDB Report Database -  Reports describing structural problems in PDB entries.
PDB Structure Quality - Determine if your structure is on-par with others in the PDB.
PDB2PQR Server - Enables a user to convert PDB files into PQR files.
Pfam - Large collection of protein families.
PIqsI - investigation and curation of quaternary structures.
PISA -  An interactive tool for the exploration of protein Interfaces, Surfaces and Assemblies.
Pre-BI - Prediction of biological interfaces.
PredictProtein - A service for sequence analysis, structure and function prediction.
Probe - Evaluate atomic packing, either within or between molecules. It generates “contact dots” where
atoms are in close contact.
ProDom - Protein domain families.
PRODRG-2 Server - Convert small molecules in PDB format to various topology formats.
ProFunc - Prediction of protein function from 3D structure; EBI services.
ProMate - Predicts the location of potential protein-protein binding sites.
PROPKA - Empirical Prediction and Interpretation of Protein pKa Values.
Protein Calculator - Protein properties calculator.
Protein Structure Prediction - Molecular modelling site.
Proteopedia - The collaborative, 3D encyclopedia of proteins and other molecules. Article
ProtSkin - Converts a protein sequence alignment to a property file used to map the
sequence conservation onto the structure of a protein.
PROTORP  - A tool to analyse the properties of interfaces of protein-protein associations.
PSAIA - Software tool  that integrates several algorithms for protein interactions and structure geometry
analysis of protein complexes into a single application.
RAPPER - An ab initio conformational search algorithm for restraint-based protein modelling.
ROBETTA - Full-chain protein structure prediction server.
SCOP - Structural classification of proteins.
SFCheck - Assessment of X-ray data and/or agreement between atomic model and X-ray data.
SPASM Server - Server will find similar motifs based in a database derived from the PDB.
SSBOND - predicts sites where disulphide bonds can be introduced.
STAN - Structure analysis server.
StrucTools - Common structural biology calculations with PDB coordinates.
SURFNET - Generates surfaces and void regions between surfaces.
TLSMD - Inference of TLS motion from single crystal structures.
TOPS - Compare a structure (PDB Format) to a database of structures.
Web-Tools - Web-Accessible Scientific Applications (scientific supercomputing at NIH).
WHAT IF - Homology modelling, drug docking, electrostatics, validation and visualisation.
3Dee - Database of Protein Domain Definitions.
3DNA - Analysis, rebuilding, and visualization of three-dimensional nucleic acid structures.

source: http://www.pxuniverse.com/Websites.html

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