Application Index

This is a collection of analysis tools for protein such as 3-D structure comparison, binding site identification, noncovalent bond finder, dimensions of pore of an ion channel etc.

SSBOND predicts locations where disulphide bonds can be introduced in proteins of known structure. It generates a list of pairs of residues that, if mutated to cysteines, will form proper disulphide bonds. The program will list the dihedral angles that describe the disulfide bond conformation and an energy estimate of the strain that is introduced.
View Application Entry for SSBOND

MSU ProFlex (formerly called FIRST) is a patented computational tool for identifying rigid and flexible regions in protein structures and protein-ligand complexes. Analysis of a single, static three-dimensional protein structure can capture the essential conformational flexibility of the protein. Hydrogen bonds, salt bridges and hydrophobic contacts are identified by geometric and energetic criteria once polar hydrogens have been placed using an external program (such as What If). Using a constraint counting algorithm, all-atom calculations on proteins of over 1000 residues can be completed within seconds. This software is available as source code and has been applied to many proteins and their complexes.
View Application Entry for ProFlex

MSU SLIDE (Screening for Ligands by Induced-fit Docking, Efficiently) represents a general approach to organic and peptidyl database screening. It can handle large binding-site templates and uses multi-stage indexing to identify feasible subsets of template points for ligand docking. An optimization approach based on mean-field theory is applied to model induced-fit complementarity, balancing flexibility between the ligand and the protein side chains.
View Application Entry for SLIDE

Sequery is a tool to search the sequences of the protein structures in the Protein Data Bank (PDB) for a particular pattern of residues, which may include exact matches and acceptable substitutions based on a user-specified amino acid substitution matrix and/or a numerical threshold. Sequery was developed by Michael E. Pique, Michael A. Siani, Leslie A. Kuhn, Elizabeth D. Getzoff, and John A. Tainer, Department of Molecular Biology, The Scripps Research Institute and is distributed here with permission of the authors.
View Application Entry for Sequery

PASS is a fast cavity-detection program for the identification and visualization of possible protein binding sites. It is freely available for Unix machines.
View Application Entry for PASS (Putative Active Sites with Spheres)

PIPSA is a tool to compute and analyze the pairwise similarity of 3D interaction property fields for a set of proteins. The interaction properties are computed from the 3D coordinates of a set of superimposed proteins. PIPSA produces a matrix of pairwise similarity indices for each protein interaction property. This matrix is converted into a distance matrix which may be used for clustering or visualization.
View Application Entry for PIPSA: Protein Interaction Property Similarity Analysis tool

ProSAT is a tool to facilitate interactive visualization of non-structure-based functional annotations in protein 3D structures. It performs automated mapping of the functional annotations onto the protein structure and allows functional sites to be readily identified upon visualization. The current version of ProSAT can be applied to large datasets of protein structures for fast visual identification of active and other functional sites derived from the SwissProt and Prosite databases.
View Application Entry for ProSAT: Protein Structure Annotation Tool

ProSAT2 is a server to select and group residue based annotations and explore them interactively on a 3D structure of a protein. The residue-based information are extracted from databases SwissProt, ProSite, BRENDA, UniProt or user defined. Visualisation is based on the WebMol, Java Protein viewer.
View Application Entry for ProSAT2: Protein Structure Annotation Server

MolSurfer is a tool that provides two-dimensional maps of protein interfaces that can be used to explore three-dimensional structures of protein complexes and their interfaces.
View Application Entry for MolSurfer

The GNU polyxmass software framework is aimed at allowing user to perform (bio-)chemical and mass spectrometric simulations on linear polymer sequences. Any polymer chemistry might be involved (proteins, saccharides, nucleic acids...) because the polyxdef module will let the user defined any polymer chemistry by himself. Once a polymer chemistry definition is elaborated, it can be used in polyxedit, the main module of the software suite, where all the polymer sequence editing and (bio-)chemical and mass spectrometric simulations are performed.
View Application Entry for GNU polyxmass

VOLUME is a program which calculates the volume of a polyhedron surrounding each atom in a protein model. The algorithm is based on the procedure described by Voroni.
View Application Entry for Volume

Occluded surface (OS) is a package of programs to calculate the occluded surface and atomic packing of protein model structures.
View Application Entry for Occluded surface (OS)

SurfVol (SURFace VOLumes) is a computer code which computes volume or surface properties of proteins.
View Application Entry for SurfVol (SURFace VOLumes)

CONCOORD is a method to generate protein conformations around a known structure based on distance restrictions. Principal component analyses of Molecular Dynamics (MD) simulations of proteins have indicated that collective degrees of freedom dominate protein conformational fluctuations. These large-scale collective motions have been shown essential to protein function in a number of cases. The notion that internal constraints and other configurational barriers restrict protein dynamics to a limited number of collective degrees of freedom has led to the design of the CONCOORD method to predict these modes without doing explicit, more CPU intensive, MD simulations.
View Application Entry for CONCOORD

Dyndom is a program that determines protein domains, hinge axes and amino acid residues involved in the hinge bending motion. It requires two conformations to perform this task. It is fully automated and applicable to multi-domain proteins.
View Application Entry for Dyndom

Mpex is a java based program that can be used to analyze membrone protein sequences for possible trans membrane sequences. The program can also calculate the free energies of partitioning of a protein between water/octanol as well as water/membrane-interface Also. it can be used to draw helical wheel diagrams.
View Application Entry for Mpex (Membrane Protein Explorer)

MODELLER is a program for homology protein structure modelling by satisfaction of spatial restraints.
View Application Entry for MODELLER

MINT is a graphical user interface to Andrej Sali Modeller program. It allows only the basic homology modelling functions of Modeller to be used, but saves you from having to use the Modeller control language. The latest MINT V3.0 is compatible with the latest version of Modeller known as Modeller-3. MINT is written in Tcl/Tk. It provides you with a simple GUI where you enter the name of your sequence file, the PDB codes being used as parents and optionallay an alignment file. A limited number of additional parameters may also be set. You then simply click the Run button to write a Modeller control file and spawn the Modeller program. MINT is freely available for use by not-for-profit organisations. Commercial use is not permitted without express permission from the author. It may not be distributed without the author permission, but must be obtained from the site. It is supplied as a gzipped tar file of Tcl/Tk code.
View Application Entry for MINT

TORSIONS is a simple program to read a PDB file and calculate backbone torsion angles. It calculates phi, psi and omega and can also calculate C-alpha pseudo-torsions.
View Application Entry for TORSIONS

This program calculates the volume of a macromolecule by a method somewhat akin to the Monte Carlo method, namely, by measuring how many vertices of a dense regular grid happen to be within the probe radius of the molecular atoms. The Volume is then calculated as V = V_grid * N_near / N_total = N_near * V_per_node.
View Application Entry for Mol_Volume

VAST Search is structure-structure similarity search service of NCBI. It compares 3D coordinates of a newly determined protein structure to those in the MMDB/PDB database. VAST Search computes a list of structure neighbors that you may browse interactively, viewing superpositions and alignments by molecular graphics.
View Application Entry for VAST (Vector Alignment Search Tool)

HOLE was written at Birkbeck College from April 1992 to allow the visualization and analysis of the holes through atomic models of ion channels. A number of people have suggested that it may prove to be useful to other scientists working on ion channel models and it is being publicly distributed with that hope. Its initial application is to four experimentally determined structures of gramicidin A.
View Application Entry for HOLE

TRITON is graphical tool for modelling protein mutants and assessment of their activities. Protein mutants are modelled based on the wild type structure by homology modelling using the external program MODELLER. Chemical reactions taking place in the mutants active site are modelled using the semi-empirical quantum mechanic program MOPAC. Semi-quantitative predictions of mutants activities can be achieved by evaluating the changes in energies of the system and partial atomic charges of the active site residues during the reaction. The program TRITON offers graphical tools for the preparation of the input data files, for calculation and for the analysis of the generated output data. Implementation ensures the overall integrity of consecutive steps of the modelling of mutants and calculation of reaction coordinates, but the program can also be used simply for combinatorial generation of multiple mutants by homology modelling.
View Application Entry for TRITON

COMPOSER module provides the tools needed for knowledge-based homology modeling of protein structures. Based on the program developed by Professor Thomas Blundell and colleagues at Birkbeck College, England, Composer uses both sequence and structural information from known families of proteins to predict the 3D structure of an unknown. It is especially useful for extracting all the structural information resident in the members of a family of homologs, and has been shown to build complete, accurate models for proteins with as low as 30% sequence homology. Composer has been shown to generate more complete, accurate models than many of its competitors. Composer is integrated into the SYBYL Molecular Modeling Environment and requires both SYBYL/Base and Biopolymer modules. Analysis of resulting models is enhanced and simplified by the ProTable module. The new GeneFold module uses Composer to build model proteins based on sequence threading technologies.
View Application Entry for COMPOSER

PDBtool supports the browsing querying and verification (mainly geometry) of macromolecular structure data as found in files from the Protein Data Back (PDB).
View Application Entry for PDBtool

NNPREDICT is a web-based program that predicts the secondary structure type for each residue in an amino acid sequence.
View Application Entry for NNPREDICT

123D is a web-based program which combines substitution matrix, secondary structure prediction, and contact capacity potentials to thread a sequence throught the set of structures.
View Application Entry for 123D

PROTARCH is a free system of programs for hierarchical prediction of protein structure based on the thermodynamic hypothesis. At present three hardware platforms are supported: IBM SP2, Linux and MS Windows NT/2000.
View Application Entry for PROTARCH

ANALYZE is free program which can analyze conformations obtained from global searches. It includes capabability to compare NMR intensites and coupling constants to experimental data. ANALYZE has been tested on IBM, IBM SP2, SUN workstations and Pentium machines running RedHat Linux. The program does not run well on SGI platforms.
View Application Entry for ANALYZE

CATH is a novel hierarchical classification of protein domain structures, which clusters proteins at four major levels, class(C), architecture(A), topology(T) and homologous superfamily (H). Class, derived from secondary structure content, is assigned for more than 90% of protein structures automatically. Architecture, which describes the gross orientation of secondary structures, independent of connectivities, is currently assigned manually. The topology level clusters structures according to their toplogical connections and numbers of secondary structures. The homologous superfamilies cluster proteins with highly similar structures and functions. The assignments of structures to toplogy families and homologous superfamilies are made by sequence and structure comparisons.
View Application Entry for CATH

MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace. The backbone is assembled from fragments taken from known structures. Side chain conformations are optimized in rotamer space using a rough potential energy function to avoid clashes.
View Application Entry for MaxSprout

IMCLite is a Molecular graphics program supporting manual docking, interactive model building, structure analysis and comparison. It is vailable for most UNIX systems, LINUX and WinNT.
View Application Entry for IMCLite

SQUID is a software for the analysis of protein structures and molecular dynamics simulations. It is free for academic research. The program can be installed onon an SGI on IRIX6.2 an higher or on a PC running Linux.
View Application Entry for SQUID

Profit is a software for fitting protein structures on to each other.
View Application Entry for Profit

The SURFNET program generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file. It can computevan der Waals surfaces, gaps between molecules, Clefts, cavities and binding sites, 3D density distributions and sidechain-sidechain interactions. This program is available free to academic institutions.
View Application Entry for SURFNET

LOOPP is a free program for PROTEIN RECOGNITION and design of PROTEIN FOLDING potentials. LOOPP (Learning, Observing and Outputting Protein Patterns) evolved from the previous LOOPP (Linear Optimization of Protein Potentials). As suggested by the new/old name there is some continuity, but there are also many new features. LOOPP is available on IBM RS/6000 and SP, Windows NT (to be run from a command prompt - no graphical interface), SGI, SUN SOLARIS and LINUX.
View Application Entry for LOOPP (Learning, Observing and Outputting Protein Patterns)

ECEPPAK is a free software which can perform the following calculations: - Single Energy Evaluation - Single Energy Minimization - Energy evaluation of Multiple Input Conformations - Energy Minimization of Multiple Input Conformations - Monte Carlo Search using a generalized MCM (EDMC) algorithm. - PRODUCE an energy map for a pair of dihedral angles. - Carry out an rms deviations analysis. - Variable Target Function Procedure for structure determination It is available on IBM RS/6000 and SP, SGI.
View Application Entry for ECEPPAK

CE and CL are web-based software for 3-D structure comparison and alignment by Combinatorial Extension (CE) and by Compound Likeness (CL) respectively.
View Application Entry for CE/CL

ESPript is a utility to generate a pretty PostScript output from aligned sequences. Its main input is an ASCII file of pre-aligned sequences. Optional files allow further rendering. The program calculates a similarity score for each residue of the aligned sequences. The program can also be run via the web site.
View Application Entry for ESPript (Easy Sequencing in Postscript)

NCBF is a free software for finding non-covalent interactions for use with Chime 2 or higher and Netscape Navigator 4.04 or later.
View Application Entry for NCBF (Noncovalent Bond Finder)

PROCHECK is a program that checks the stereochemical quality of a protein structure. It is free and is available for Unix or Windows NT.
View Application Entry for PROCHECK

SARF is a free program which searches for similar structural motifs in protein structures via an analysis of backbone fragments. If the two proteins are in the PDB then the program can also be run directly from the website. Otherwise it has to be downloaded to your local machine. PLATFORM : SGI or DEC computer; If the two proteins are in the PDB then it can be run directly from any computer having a web browser.
View Application Entry for SARF (Spatial ARrangement of backbone Fragments)

TOP is a free program which compares protein structures and performs 3d database search. The program is written in standard FORTRAN 77 so in principle the executable code can be installed on any computers with FORTRAN compiler, hing via Internet. A server system has also been built up for running the program via Web.
View Application Entry for TOP (protein TOPological comparison program)

WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc. It is available commercially for unix and windows users.
View Application Entry for WHAT IF

WHAT_CHECK is a system for protein structure validation derived from the WHAT IF program. This program is available for free and can be used on Silicon Graphics machine or DEC ALPHA running OSF/1.
View Application Entry for WHAT_CHECK