Protein Crystallography Structure Analysis
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Visualization
BOBScript - Robert Esnouf's extensions to MolScript version 1.4
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.
MolScript - program for displaying molecular 3D structures, such as proteins, in both schematic and
detailed representations.
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
Abysis - Protein Sequence and Structure Analysis of Antibody Variable Domains.
Aline - An extensible WYSIWYG protein sequence alignment editor for publication quality figures.
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.
FFAS - Fold & Function Assignment System (good for building models for low homology MR searches.
A relevant paper: 2004 Acta Cryst D60 1229-1236.)
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
SCOPPI - Structural Classification of Protein-Protein Interfaces (Dresden Univ. of Technology)
SSM - Secondary Structure Matching: a tool for protein structure comparison
Stralign - Structure alignment program.
STRAP - Structure based alignment program (Christoph Gille).
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.
Bioinformatics Toolkit - a platform that integrates a great variety of tools for protein sequence
analysis - Max-Planck Institute for Developmental Biology.
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.
COPS -(Classification Of Protein Structures) web server which is a next-generation web application that
provides fast and intuitive access to the entire set of currently available protein structures. COPS
organizes structural domains by quantified structural similarities which can be visualized immediately
with Jmol. Additionally, structural biologists can employ iCOPS to classify their own structures.
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.
MACiE - contains 223 fully annotated enzyme reaction mechanisms (Janet Thornton)
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.
NQ-Flipper - Validates and corrects asparagine and glutamine side-chain amide rotamers in protein
structures. An interactive Jmol applet highlights the most offending interactions between atom pairs.
OCA - A browser-database for protein structure/function.
OnD-CRF - Order and Disorder in proteins prediction server.
Parvati - Protein Anisotropic Refinement Validation and Analysis Tool
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 - Recognition of spatial motifs in protein structures.
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.
BOBScript - Robert Esnouf's extensions to MolScript version 1.4
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.
MolScript - program for displaying molecular 3D structures, such as proteins, in both schematic and
detailed representations.
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
Abysis - Protein Sequence and Structure Analysis of Antibody Variable Domains.
Aline - An extensible WYSIWYG protein sequence alignment editor for publication quality figures.
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.
FFAS - Fold & Function Assignment System (good for building models for low homology MR searches.
A relevant paper: 2004 Acta Cryst D60 1229-1236.)
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
SCOPPI - Structural Classification of Protein-Protein Interfaces (Dresden Univ. of Technology)
SSM - Secondary Structure Matching: a tool for protein structure comparison
Stralign - Structure alignment program.
STRAP - Structure based alignment program (Christoph Gille).
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.
Bioinformatics Toolkit - a platform that integrates a great variety of tools for protein sequence
analysis - Max-Planck Institute for Developmental Biology.
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.
COPS -(Classification Of Protein Structures) web server which is a next-generation web application that
provides fast and intuitive access to the entire set of currently available protein structures. COPS
organizes structural domains by quantified structural similarities which can be visualized immediately
with Jmol. Additionally, structural biologists can employ iCOPS to classify their own structures.
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.
MACiE - contains 223 fully annotated enzyme reaction mechanisms (Janet Thornton)
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.
NQ-Flipper - Validates and corrects asparagine and glutamine side-chain amide rotamers in protein
structures. An interactive Jmol applet highlights the most offending interactions between atom pairs.
OCA - A browser-database for protein structure/function.
OnD-CRF - Order and Disorder in proteins prediction server.
Parvati - Protein Anisotropic Refinement Validation and Analysis Tool
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 - Recognition of spatial motifs in protein structures.
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.