Protein Structural Prediction

|| Browse

Internet Resources

Computational & Web Resources

Downloadable Software


Structural Biology

Molecular Modeling

Protein Structural Prediction

2nd Window Opens resource in a 2nd browser window.

2nd Window
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].

[more info][11227]

2nd Window
[PBIL] A package of methods designed for the estimation of protein sequence secondary structure.

[more info][11217]

2nd Window
DomainFinder 1.0
[K. Hinsen] (Centre National de la Recherche Scientifique) A program for the determination and characterization of dynamical domains in proteins.

[more info][11218]

2nd Window
[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.

[more info][11219]

2nd Window
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).”

[more info][12258]

2nd Window
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.

[more info][11221]

2nd Window
Macromolecular Geometry
[Yale Bioinformatics] A library of source code for doing a variety of calculations on protein structures and sequences.

[more info][11222]

2nd Window
[University of Montreal] This program determines 3D protein and RNA structures.

[more info][11223]

2nd Window
[Rockefeller Univ.] A program for homology protein structure modelling by satisfaction of spatial restraints.

[more info][11224]

2nd Window
PHD Secondary Structure Software ftp Site
[Columbia University] [Annotation pending]

[more info][12265]

Top of Page

2nd Window
[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.

[more info][11225]

2nd Window
[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.

[more info][11226]

2nd Window
[A.R. Crofts, Univ. of Illinois] Assists in analysis of protein sequences for information about secondary and tertiary structure.

[more info][11228]

2nd Window
P-SEA Software
[LMCP] This software assigns secondary structure elements in protein structures from the Ca trace of Labesse, et al. CABIOS, vol 13., no. 3.

[more info][12274]

2nd Window
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.

[more info][11229]

2nd Window
[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.

[more info][11231]

2nd Window
Swiss Pdb-Viewer
[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.

[more info][11144]

2nd Window
[Purdue Univ.] Protein topological comparison program that can detect similarities between two protein structures.

[more info][10520]