Structure Analysis

SBGrid supports 44 structure analysis software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title Description Linux 32-bit Linux 64-bit OS X Intel Links

3DNA

- a package for analyzing, visualizing and rebuilding 3-dimensional nucleic acid structures. 3DNA was created by Dr. Xiang-Jun ...

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  • a package for analyzing, visualizing and rebuilding 3-dimensional nucleic acid structures. 3DNA was created by Dr. Xiang-Jun Lu in the laboratory of Professor Wilma K. Olson at the Department of Chemistry and Chemical Biology, Rutgers-the State University of New Jersey.

Developers

Wilma Olson

Xiang-Jun Lu

Categories

X-ray Crystallography

Structure Analysis

Structure Visualization

Nucleic Acids

Versions

Citations

Xiang-Jun Lu and Wilma K Olson (2008) "3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures." Nature Protocols, 3, 1213-1227.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid 3DNA page.

APBS

- a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE). This software was written ...

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  • a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE). This software was written by Nathan Baker in collaboration with J. Andrew McCammon and Michael Holst and enhanced by several others.

Developers

Michael Holst

Nathan Baker

Categories

Structure Analysis

Versions

Citations

Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001.

License Type

This software is distributed under an Open license.


Static link to the SBGrid APBS page.

AQUA

- a suite of programs that analyze the quality of biomolecular structures determined via NMR spectroscopy. AQUA was ...

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  • a suite of programs that analyze the quality of biomolecular structures determined via NMR spectroscopy. AQUA was initially developed by Ton Rullmann and Jurgen Doreleijersb Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands. Current maintenance and expansion by Jurgen Doreleijers, BioMagResBank, University of Wisconsin-Madison, USA.

Developers

Jurgen Doreleijers

Categories

NMR Methods

Structure Analysis

Versions

Citations

Laskowski R.A., Rullmann J.A.C., MacArthur M.W., Kaptein R. & Thornton J.M. (1996). "AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR". J. Biomol. NMR 8, 477-486.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid AQUA page.

CMView

- an interactive contact map visualization and analysis tool that supports assessing similarities and differences between structure- or ...

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  • an interactive contact map visualization and analysis tool that supports assessing similarities and differences between structure- or contact predictions.

Developers

Michael Lappe

Categories

Structure Analysis

Structure Visualization

Versions

Citations

Vehlow et al. CMView: interactive contact map visualization and analysis. Bioinformatics (2011) vol. 27 (11) pp. 1573-4

License Type

This software is distributed under an Open license.


Static link to the SBGrid CMView page.

CURVES

- an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to ...

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  • an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis.

Developers

Richard Lavery

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Lavery and Sklenar. Defining the structure of irregular nucleic acids: conventions and principles. J Biomol Struct Dyn (1989) vol. 6 (4) pp. 655-67

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid CURVES page.

Curves+

- a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the ...

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  • a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the helper programs Canal, Cdif and Sumr.

Developers

Richard Lavery

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Lavery et al. Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res (2009) vol. 37 (17) pp. 5917-29

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid Curves+ page.

DELPHI

- a program for calculating protein electrostatics.

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  • a program for calculating protein electrostatics.

Developers

Barry Honig

Categories

Structure Analysis

Versions

Citations

Rocchia et al. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem (2002) vol. 23 (1) pp. 128-37

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid DELPHI page.

Dowser

- a program that surveys a protein molecule's structure to locate internal cavities and assess the hydrophilicity of ...

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  • a program that surveys a protein molecule's structure to locate internal cavities and assess the hydrophilicity of those cavities in terms of the energy of interaction of a water molecule with the surrounding atoms. Experience has shown that cavities with interaction energies below -12 kcal/mol tend to be filled, and cavities for which the energy is above that threshold, tend to be empty.

Developers

Jan Hermans

Categories

Structure Analysis

Versions

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid Dowser page.

DSSP

- a program that standardizes secondary structure assignment calculated from a coordinate file. Secondary structure prediction is not ...

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  • a program that standardizes secondary structure assignment calculated from a coordinate file. Secondary structure prediction is not supported. Designed by Wolfgang Kabsch and Chris Sander

Developers

Gert Vriend

Categories

Structure Analysis

Versions

Citations

Kabsch and Sander. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) vol. 22 (12) pp. 2577-637

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid DSSP page.

DynDom

- a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are ...

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  • a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.

Developers

Steven Hayward

Categories

Structure Analysis

Versions

Citations

Hayward and Lee. Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J Mol Graph Model (2002) vol. 21 (3) pp. 181-3

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid DynDom page.

ENTANGLE

- a JAVA program that reads PDB files containing a nucleic-acid protein complex and gives a listing of ...

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  • a JAVA program that reads PDB files containing a nucleic-acid protein complex and gives 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. Entangle also recognizes when a stacking interaction occurs between two aromatic residues. In addition to a listing, Entangle allows the user to probe the interface in three-dimensions.

Developers

Yousif Shamoo

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Allers and Shamoo. Structure-based analysis of protein-RNA interactions using the program ENTANGLE. Journal of molecular biology (2001) vol. 311 (1) pp. 75-86

Technical Notes

Not all PDBs work with this program.

Some example PDBs that work:
1URW
1CVJ

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid ENTANGLE page.

ESCET

- a script driven program that analyzes and compares three-dimensional protein structures. The current version (0.7) is mostly ...

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  • a script driven program that analyzes and compares three-dimensional protein structures. The current version (0.7) is mostly designed to find the rigid part of protein molecules by comparing different structures.

Developers

Thomas Schneider

Categories

Structure Analysis

Versions

Citations

Schneider. Domain identification by iterative analysis of error-scaled difference distance matrices. Acta crystallographica Section D, Biological crystallography (2004) vol. 60 (Pt 12 Pt 1) pp. 2269-75

Schneider. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta crystallographica Section D, Biological crystallography (2002) vol. 58 (Pt 2) pp. 195-208

Schneider. Objective comparison of protein structures: error-scaled difference distance matrices. Acta crystallographica Section D, Biological crystallography (2000) vol. 56 (Pt 6) pp. 714-21

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid ESCET page.

ESPript

- (Easy Sequencing in Postscript) is a utility to generate a pretty PostScript output from aligned sequences and ...

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  • (Easy Sequencing in Postscript) is a utility to generate a pretty PostScript output from aligned sequences and coordinate files.

Developers

Xavier ROBERT

Categories

Structure Analysis

Structure Visualization

Versions

Citations

Gouet et al. ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic acids research (2003) vol. 31 (13) pp. 3320-3

Gouet et al. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics (Oxford, England) (1999) vol. 15 (4) pp. 305-8

License Type

This software is distributed under an Academic license.


Static link to the SBGrid ESPript page.

GRASP

- a molecular visualization and analysis program supported on SGIs. It is particularly useful for the display and ...

  • a molecular visualization and analysis program supported on SGIs. It is particularly useful for the display and manipulation of surfaces of molecules and their electrostatic properties.

Developers

Barry Honig

Categories

Structure Analysis

Structure Visualization

Versions

Citations

Anthony Nicholls, Kim Sharp and Barry Honig, PROTEINS, Structure, Function and Genetics, Vol. 11, No.4, 1991, pg. 281ff

Technical Notes

You can convert grasp surface to raster3d format using ungrasp utility (runs only on SGIs).

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid GRASP page.

HBPLUS

- a program suite (hbplus, access and clean) to compute hydrogen positions, hydrogen bonds, and neighboring interactions. The ...

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  • a program suite (hbplus, access and clean) to compute hydrogen positions, hydrogen bonds, and neighboring interactions. The application was developed at University College London.

Developers

Roman Laskowski

Categories

Structure Analysis

Versions

Citations

McDonald and Thornton. Satisfying hydrogen bonding potential in proteins. Journal of molecular biology (1994) vol. 238 (5) pp. 777-93

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid HBPLUS page.

HOLE

- a program that allows the analysis and visualisation of the pore dimensions of the holes through molecular ...

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  • a program that allows the analysis and visualisation of the pore dimensions of the holes through molecular structures of ion channels. The application was developed by Oliver S. Smart, and is currently hosted by the Sansom Laboratory at the University of Oxford.

Developers

Oliver Smart

Categories

Structure Analysis

Versions

Citations

Smart et al. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. Journal of molecular graphics. 1996. 14 (6): 354-60, 376.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid HOLE page.

LIGPLOT

- a program for automatically plotting protein-ligand interactions.

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  • a program for automatically plotting protein-ligand interactions.

Developers

Roman Laskowski

Categories

Structure Analysis

Versions

Citations

Wallace et al. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng (1995) vol. 8 (2) pp. 127-34

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid LIGPLOT page.

LigPlot+

- a graphical front-end to the LIGPLOT (protein-ligand interactions) and DIMPLOT (protein-protein, domain-domain interactions) programs. The plots generated ...

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  • a graphical front-end to the LIGPLOT (protein-ligand interactions) and DIMPLOT (protein-protein, domain-domain interactions) programs. The plots generated by these programs can be interactively edited on screen, superposed and printed.

Developers

Roman Laskowski

Categories

Structure Analysis

Versions

Citations

Wallace et al. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng (1995) vol. 8 (2) pp. 127-34

License Type

This software is distributed under an Academic license.


Static link to the SBGrid LigPlot+ page.

Madbend

- a program for calculating the curvature of nucleic acids. From a given list of base pair step ...

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  • a program for calculating the curvature of nucleic acids. From a given list of base pair step roll, tilt and twist values, and the specification of a reference plane, the program produces the global tilt, global roll and the bend magnitude. These quantities thus describe the direction and magnitude of a bend angle and can be used to analyze DNA and DNA/protein complex geometries.

Developers

Dan Strahs

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Barbic and Crothers. Comparison of analyses of DNA curvature. J Biomol Struct Dyn (2003) vol. 21 (1) pp. 89-97

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid Madbend page.

MAMMOTH-Mult

- a package that does multiple alignment of protein structures, providing a common 3D superimposition, a corresponding structure-based ...

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  • a package that does multiple alignment of protein structures, providing a common 3D superimposition, a corresponding structure-based sequence alignment and a dendrogram for the set of structures aligned.

Developers

Dmitry Lupyan

Categories

Structure Analysis

Versions

Citations

Lupyan et al. A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics. 2005. 21(15):3255-63.

License Type

This software is distributed under an Academic license.


Static link to the SBGrid MAMMOTH-Mult page.

Maxit

- was developed by the PDB (Protein Data Bank) and NDB (Nucleic Acid Database) to assist in the ...

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  • was developed by the PDB (Protein Data Bank) and NDB (Nucleic Acid Database) to assist in the processing and curation of macromolecular structure data. Features include reading and writing PDB and mmCIF format files, and translating between file formats.

Developers

RCSB Developer Group

Categories

Structure Analysis

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid Maxit page.

MCCE

- Multi-Conformation Continuum Electrostatics) is a biophysics simulation program combining continuum electrostatics and molecular mechanics. In this program, ...

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  • Multi-Conformation Continuum Electrostatics) is a biophysics simulation program combining continuum electrostatics and molecular mechanics. In this program, the protein side chain motions are simulated explicitly while the dielectric effect of solvent and bulk protein material is modeled by continuum electrostatics.

Developers

MCCE Developer Group

Marilyn Gunner

Categories

Structure Analysis

Versions

Citations

Song et al. MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling. Journal of computational chemistry (2009) vol. 30 (14) pp. 2231-47

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid MCCE page.

Mead

- a program that is used for including solvation effects in biological systems, such as proteins, using an ...

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  • a program that is used for including solvation effects in biological systems, such as proteins, using an atomic model of the protein. This is done by solving the Poisson-Boltzmann equation in a dielectric medium, including distributed point charges on a grid.

Developers

Donald Bashford

Categories

Structure Analysis

Versions

Citations

Bashford and Gerwert. Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin. Journal of molecular biology (1992) vol. 224 (2) pp. 473-86

License Type

This software is distributed under an Open license.


Static link to the SBGrid Mead page.

MOLE

- a universal toolkit for rapid and fully automated location and characterization of channels and pores in molecular ...

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  • a universal toolkit for rapid and fully automated location and characterization of channels and pores in molecular structures. The core of the MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. MOLE is a powerful software program for exploring large molecular channels, complex networks of channels and molecular dynamics trajectories in which analysis of a large number of snapshots is required.

Developers

Michal Otyepka

Martin Petrek

Categories

Structure Analysis

Versions

Citations

Petrek et al. MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure (London, England : 1993) (2007) vol. 15 (11) pp. 1357-63

Petrek et al. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC bioinformatics (2006) vol. 7 pp. 316

License Type

This software is distributed under an Open license.


Static link to the SBGrid MOLE page.

NACCESS

- a stand-alone program that calculates the accessible area of a molecule from a PDB format file.

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  • a stand-alone program that calculates the accessible area of a molecule from a PDB format file.

Developers

Simon Hubbard

Categories

Structure Analysis

Versions

Citations

Hubbard, S.J. & Thornton, J.M. (1993), "NACCESS", Computer Program, Department of Biochemistry and Molecular Biology, University College London.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid NACCESS page.

NUCPLOT

- a program to generate schematic diagrams of protein-DNA interactions. The program works for any single- or double-stranded ...

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  • a program to generate schematic diagrams of protein-DNA interactions. The program works for any single- or double-stranded protein-DNA, DNA-ligand and protein-RNA complexes.

Developers

Roman Laskowski

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Luscombe N M, Laskowski R A, Thornton J M. NUCPLOT: a program to generate schematic diagams of protein-DNA interactions. Nucleic Acids Research. 1997. 25:4940-4945.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid NUCPLOT page.

Probe

- an application to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms ...

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  • an application to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file.

Developers

Jane Richardson

David Richardson

Categories

Structure Analysis

Utilities

Versions

Citations

Word et al. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. Journal of molecular biology (1999) vol. 285 (4) pp. 1711-33

License Type

This software is distributed under an Open license.


Static link to the SBGrid Probe page.

PROCHECK

- checks the stereochemical quality of a protein structure, producing a number of PostScript plots analyzing its overall ...

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  • checks the stereochemical quality of a protein structure, producing a number of PostScript plots analyzing its overall and residue-by-residue geometry.

Developers

Roman Laskowski

Categories

Structure Analysis

Versions

Citations

Laskowski R A, MacArthur M W, Moss D S & Thornton J M (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 26, 283-291

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid PROCHECK page.

ProFit

- the ultimate protein least squares fitting program.

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  • the ultimate protein least squares fitting program.

Developers

Andrew Martin

Categories

Structure Analysis

Versions

Citations

How to cite: Fitting was performed using the McLachlan algorithm (McLachlan, A.D., 1982. Rapid Comparison of Protein Structres, Acta Cryst A38, 871-873) as implemented in the program ProFit (Martin, A.C.R., http://www.bioinf.org.uk/software/profit/).

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid ProFit page.

Qnifft

- software for macromolecular electrostatics.

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  • software for macromolecular electrostatics.

Developers

Kim Sharp

Categories

Structure Analysis

Versions

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid Qnifft page.

QPack

- a "quick" evaluation of steric packing in protein structures. Amino acid side chains are not represented in ...

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  • a "quick" evaluation of steric packing in protein structures. Amino acid side chains are not represented in full atomic detail. Instead, one or more averaged centers of interaction per residue are used. A measure of the quality of side chain packing is determined from the available spherical space available to each residue. Additionally, an empirical pairwise residue contact potential can be used to estimate the correctness of model protein structures.

Developers

Fred Cohen

Categories

Structure Analysis

Versions

Citations

Gregoret and Cohen. Novel method for the rapid evaluation of packing in protein structures. J Mol Biol (1990) vol. 211 (4) pp. 959-74

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid QPack page.

QUILT

- detects contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.

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  • detects contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.

Developers

Philip Lijnzaad

Categories

Structure Analysis

Versions

Citations

Lijnzaad et al. On defining the dynamics of hydrophobic patches on protein surfaces. Proteins (2008) vol. 72 (1) pp. 105-14

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid QUILT page.

RNAView

- a program is developed to quickly display the secondary structure of RNA/DNA with tertiary interactions. It is ...

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  • a program is developed to quickly display the secondary structure of RNA/DNA with tertiary interactions. It is fully implemented with Leontis and Westhof's ( RNA (2001) 7, 499-512), convention for the edge-to-edge hydrogen bonding interactions.

Developers

RNAVIEW Developer Group

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Yang et al. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 2003. 31(13):3450-60

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid RNAView page.

STAMP

- (STructural Alignment of Multiple Proteins) a suite of programs for the comparison and alignment of protein three ...

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  • (STructural Alignment of Multiple Proteins) a suite of programs for the comparison and alignment of protein three dimensional structures. The suite will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. The software will also search a database of protein structures to identify structurally similar proteins. The suite includes a number of utility programs for the manipulation of protein structures.

Developers

Geoff Barton

Categories

Structure Analysis

Versions

Citations

Russell & Barton. Multiple protein sequence alignment from tertiary structure comparison, PROTEINS: Struct. Funct. Genet. 1992. 14: 309-323.

License Type

This software is distributed under an Open license.


Static link to the SBGrid STAMP page.

Surface Racer

- calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules. The ...

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  • calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules. The program also analyzes cavities in the protein interior inaccessible to solvent from outside.

Developers

Oleg Tsodikov

Categories

Structure Analysis

Versions

Citations

Tsodikov et al. A novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J. Comput. Chem. 2002. 23:600-609.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid Surface Racer page.

SURFNET

- a program that generates surfaces, density contours and gap regions from coordinate data supplied in a PDB ...

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  • a program that generates surfaces, density contours and gap regions from coordinate data supplied in a PDB file.

Developers

Roman Laskowski

Categories

Structure Analysis

Versions

Citations

Confidentiality agreement is signed and redistribution to member laboratories is fine. There is no need to send a list of users.

Laskowski. SURFNET: A program for visualizing molecular surfaces, cavities and intermolecular interactions. J. Mol. Graph. 1995. 13: 323-330.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid SURFNET page.

surfv

- calculates solvent accessible area that is defined by a probe as it rolls on the surface of ...

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  • calculates solvent accessible area that is defined by a probe as it rolls on the surface of the molecule. Thus use of a zero radius probe will give the Van der Walls surface area.

Developers

SURFace Developer Group

Categories

Structure Analysis

Versions

Citations

Sridharan et al. A new vertex algorithm to calculate solvent accessible surface areas. Biophys J. 1992. 61:A174.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid surfv page.

Swiss-PdbViewer

- an application that provides a user friendly interface allowing you to analyze several proteins at the same ...

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  • an application that provides a user friendly interface allowing you to analyze several proteins at the same time.

Developers

Nicolas Guex

Torsten Schwede

Categories

Structure Analysis

Versions

Citations

Guex and Peitsch.SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis. 1997. 18:2714-2723.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid Swiss-PdbViewer page.

Theseus

- a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus finds ...

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  • a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood. By downweighting variable regions of the superposition and by correcting for correlations among atoms, the ML superpositioning method produces much more accurate results.

Developers

Douglas Theobald

Categories

Structure Analysis

Versions

Citations

Theobald & Wuttke. Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem. PNAS. 2006a. 103(49):18521-18527. Theobald et al. THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures. Bioinformatics. 2006b. 22(17):2171-2172. Theobald et al. Accurate structural correlations from maximum likelihood superpositions. PLOS Computational Biology. 2008. 4(2):e43.

Technical Notes

Member labs have permission to access Theseus.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid Theseus page.

TOPS

- a system for visualization, database searching, comparison and machine learning of protein structural topology. The project has ...

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  • a system for visualization, database searching, comparison and machine learning of protein structural topology. The project has created a database of protein protein topology, enhanced with sequence and function-related information. Fast and efficient algorithms have been developed for structure comparison, motif discovery and pattern matching, and versions are being developed to include sequence and function information. Visualization facilities for TOPS diagrams have also been developed. The most speculative part of the project, is the investigation of machine learning for structure-sequence-function relationships, which aims to learn patterns linking topology to sequence, and topology and sequence to function. Interesting results will be valuable to efforts to predict protein structure and function from sequences, and these problems remain key challenges of direct relevance to projects in structural and functional genomics.

Developers

David Westhead

David Brunel

Categories

Structure Analysis

Versions

Citations

Westhead et al. Protein structural topology: automated analysis, diagrammatic representation and database searching. Protein Sci. 1999. 8(4):897-904.

Gilbert. Motif-based searching in TOPS protein topology databases. Bioinformatics. 1999. 15(4):317-26.

License Type

This software is distributed under an Open license.


Static link to the SBGrid TOPS page.

USF Gerard Utilities

- the Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, ...

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  • the Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM.

Developers

Gerard Kleywegt

Categories

X-ray Crystallography

Structure Analysis

Versions

Citations

See list of literature references here: http://www.hhmi.swmed.edu/Manuals/gerard/gerard_manuals.html

License Type

This software is distributed under an Open license.


Static link to the SBGrid USF Gerard Utilities page.

WASP

- searches PDB files for misidentified water molecules that should be modeled as cations.

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  • searches PDB files for misidentified water molecules that should be modeled as cations.

Developers

Enrico DiCera

Categories

X-ray Crystallography

Structure Analysis

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid WASP page.

WHATIF

- a general protein analysis program.

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  • a general protein analysis program.

Developers

Gert Vriend

Categories

Structure Analysis

Versions

Citations

Vriend. WHAT IF: A molecular modeling and drug design program. J. Mol. Graph. 1990. 8: 52-56.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid WHATIF page.

WHAT_CHECK

- the protein verification tool from the WHAT IF program available as a free stand-alone program, complete with ...

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  • the protein verification tool from the WHAT IF program available as a free stand-alone program, complete with all source code.

Developers

Gert Vriend

Categories

Structure Analysis

Versions

Citations

Hooft et al. Errors in protein structures. Nature. 1996. 381: 272.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid WHAT_CHECK page.