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Gene finding
Gene finding with similarity
Gene finding in Bacteria
Gene finding in Viruses
Next Generation
Gene search
Gene explorer
Promoter
Protein location
RNA structure
Protein structure
PSSFinder  prediction of protein secondary structure using Markov chains.
SSPRED  program of secondary structure prediction
SSPAL  Nearest-neighbor with local alignments SS prediction
NNSSP  Nearest-neighbor SS prediction
SSP  Segment-oriented SS prediction
SSENVID  Protein secondary structure and environment assignment from atomic coordinates
PDISORDER  Protein Disorder Prediction
GETATOMS  Atomic coordinates using homologous protein
3D-comp  Structure Alignment to Superposition
AbIni3D  Ab inition folding
MDynSB  Program MDynSB is designed to perform multiple tasks with protein structure
HMod3DMM  Energy minimization program by molecular mechanic
CYS_REC   Prediction of SS-bonding States of Cysteines in Protein Sequences
3D-Match  Comparing 3D structures of two proteins
3D-MatchDB  Comparing 3D structure with 3D-Database
3DmodelFit  program for comparison protein 3D model and its original structure
3d-explorer
SeqMan
Multiple alignment
Analysis of expression data
Plant promoter database
Search and map repeats
Extracting known SNPs

 

 

GETATOMS

Optimization of replaced side chain groups by simulated annealing algorithm

Example

Enter PDB Identifier or file in PDB format: Chain:
Enter alignment file (from screen or from file): Alignment format:

SA Temperature: Add H-atoms at the end of optimization
SA Maximal number of steps: Process loops and insertions
Use visualization  (Java3d Installation page). Note. To run applet viewer you need to include linux1.softberry.com in the list of your browser (see instruction).

[Help] [Program's page]
[Example with visualization]

[3D-Explorer help (English)] [3D-Explorer help (Russian)]

[Getpdb]

You need to JRE and Java3d has been installed on your computer for the normal work of 3d-Explorer.

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Last modification date: 19 Mar 2015

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