Structure Analysis

SBGrid supports 42 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 Lu in the laboratory of Professor Wilma K. Olson at the Department of Chemistry and Chemical Biology, Rutgers-the State University of New Jersey.

yes yes yes

APBS

- 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.

yes yes yes

AQUA

- 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.

yes yes yes

CMView

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

yes yes yes

Curves+

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

yes yes yes

CURVES

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

yes yes yes

DelPhi

A program for calculating protein electrostatics. <br><br> DelPhi is freely available to non-profit labs, but each lab must register with Columbia before we can install the software. To include this software in your installation, please register here <a href = "https://bhapp.c2b2.columbia.edu/software/cgi-bin/software.pl?input=DelPhi">https://bhapp.c2b2.columbia.edu/software/cgi-bin/software.pl?input=DelPhi</a>, then send a copy of your registration confirmation to us at <a href = "mailto:licensing@sbgrid.org">licensing@sbgrid.org</a>. <br><br>

yes yes yes

Dowser

- 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.

yes yes yes

DSSP

- 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

yes yes yes

DynDom

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

yes yes yes

ENTANGLE

- 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.

yes yes yes

ESCET

- 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. <br><br> ESCET is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register here <a href = "http://www-db.embl.de/jss/EmblGroupsOrg/mail_1.html?addressName=pers_4572&designID=121">http://www-db.embl.de/jss/EmblGroupsOrg/mail_1.html?addressName=pers_4572&designID=121</a>, then send a copy of your registration confirmation to us at <a href = "mailto:licensing@sbgrid.org">licensing@sbgrid.org</a>. <br><br>

yes yes

ESPript

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

yes yes yes

HBPLUS

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

yes yes yes

HOLE

- 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.

yes yes yes

LigPlot+

- 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.

yes yes yes

LIGPLOT

- a program for automatically plotting protein-ligand interactions.

yes yes yes

MadBend

- 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.

yes yes

MAMMOTH-Mult

- 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.

yes yes yes

Maxit

- 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.

yes yes yes

MCCE

- 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.

yes yes yes

Mead

- 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.

yes yes yes

MOLE

- 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.

yes yes yes

NACCESS

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

yes yes yes

NUCPLOT

- 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.

yes yes yes

Probe

- 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.

yes yes yes

PROCHECK

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

yes yes yes

ProFit

- the ultimate protein least squares fitting program.

yes yes yes

Qnifft

- software for macromolecular electrostatics.

yes yes yes

QPack

- 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.

yes yes yes

QUILT

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

yes yes yes

RNAView

- 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.

yes yes yes

STAMP

- (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.

yes yes yes

Surface Racer

- 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.

yes yes yes

SURFNET

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

yes yes yes

surfv

- 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.

yes yes yes

Swiss-PdbViewer

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

yes yes yes

Theseus

- 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.

yes yes yes

USF Gerard Utilities

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

yes yes yes

WASP

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

yes yes yes

WHAT_CHECK

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

yes yes yes

WHATIF

- a general protein analysis program.

yes yes