Computational & Web Resources
Protein Structural Prediction
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CAME: Center of Applied Molecular Engineering
[Institute of Chemistry and Biochemistry, University of Salzburg] CAME offers a variety of internet services such as: a protein structure superimposition server [ProSup], the structural genome annotation for C. elegans [WILMA], and a protein structure analysis tool [PROSAII].
[PBIL] A package of methods designed for the estimation of protein sequence secondary structure.
[K. Hinsen] (Centre National de la Recherche Scientifique) A program for the determination and characterization of dynamical domains in proteins.
[Univ. of North Carolina] The Dowser program surveys a protein molecule's structure to locate internal cavities and assess the hydrophilicity of these cavities in terms of the energy of interaction of a water molecule with the surrounding atoms.
DSSP Source Code
[CMBI] "The DSSP database is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB)."
FANTOM: Fast Newton-Raphson Torsion Angle Minimizer
[National Science Foundation] A program that calculates low-energy conformations of polypeptides and proteins compatible with distance and dihedral angle constraints.
[Yale Bioinformatics] A library of source code for doing a variety of calculations on protein structures and sequences.
[University of Montreal] This program determines 3D protein and RNA structures.
[Rockefeller Univ.] A program for homology protein structure modelling by satisfaction of spatial restraints.
PHD Secondary Structure Software ftp Site
[Columbia University] [Annotation pending]
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[Alexey M. Eroshkin] This software is used in the analysis of multiple protein alignments and in the study of structure-function and structure-activity relationships in protein/peptide families.
[R. Laskowski, Univ. College London] Checks the stereochemical quality of protein structure producing a number of PostScript plots analysing its overall and residue-by-residue geometry.
[A.R. Crofts, Univ. of Illinois] Assists in analysis of protein sequences for information about secondary and tertiary structure.
[LMCP] This software assigns secondary structure elements in protein structures from the Ca trace of Labesse, et al. CABIOS, vol 13., no. 3.
SARF2: Spatial ARangement of backbone Fragments
[National Cancer Institute] This is a program (server and downloadable) for spatial arrangement of backbone fragments in protein structures. The goal is to detect 3D similarities of the backbone fragments, without topological restrictions. The idea of the method is to find all the compatible (superimposable) secondary structure elements, and then to form the large ensembles of
mutually compatible elements.
[The Barton Group] 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.
[ExPASy] This program can display several molecules simultaneously. Each molecule is loaded into a individual layer and grouped according to its atomic composition and respective coordinates.
[Purdue Univ.] Protein topological comparison program that can detect similarities between two protein structures.