:: DESCRIPTION
DireX is a software to generate ensembles of protein structures that are in agreement with low resolution or sparse experimental data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
G.F.Schröder, A.T.Brunger, and M.Levitt
‘Combining Efficient Conformational Sampling with a Deformable Elastic Network Model Facilitates Structure Refinement at Low Resolution‘
Structure, Vol 15, 1630-1641 (2007)
:: DESCRIPTION
FOLDALIGN: Pairwise local and global structural alignment of RNA sequences.
FOLDALIGNM: Multiple glo-bal struc-tu-ral a-lign-ment of RNA se-quences
::DEVELOPER
Center for non-coding RNA in Technology and Health (RTH)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.
Sundfeld D, Havgaard JH, de Melo AC, Gorodkin J.
Bioinformatics. 2015 Dec 24. pii: btv748.
Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix,
Havgaard JH, Torarinsson E, Gorodkin J. PLOS computational biology. 3:e193, 2007
Multiple structural alignment and clustering of RNA sequences,
Torarinsson E, Havgaard JH, Gorodkin J. Bioinformatics. 23:926-32, 2007
:: DESCRIPTION
InfMod3DGen is a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2015 Apr 30;43(8):e54. doi: 10.1093/nar/gkv100.
Inferential modeling of 3D chromatin structure.
Wang S, Xu J, Zeng J.
:: DESCRIPTION
SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank (PDB). The resultant multiple alignment can be coloured according to different structural features and the matching 3D structures can be superimposed and viewed in RasMol.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Protein Eng. 1998 Oct;11(10):855-9.
Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis.
Milburn D, Laskowski RA, Thornton JM.
:: DESCRIPTION
XDrawChem is a two-dimensional molecule drawing program. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.
::DEVELOPER
Bryan Herger , bherger@users.sourceforge.net
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
This is FTProd, a plugin for VMD designed to characterize and identify cross-structural ‘hot spots’ in proteins. The program FTMAP identifies these druggable hot spots by docking a series of small molecular probes onto the protein surfaces. FTProd combines these output structures, clusters them, and displays them visually for easy comparison.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Feb 1;29(3):393-4. doi: 10.1093/bioinformatics/bts689. Epub 2012 Nov 29.
Multistructural hot spot characterization with FTProd.
Votapka L, Amaro RE.
:: DESCRIPTION
Amino Acid Tutor is a great tool to learn amino acid structures and codes (single letter abbreviations). You will get different types of questions, so the learning process will not be boring.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GenRGenS is a software dedicated to random generation of genomics sequences that supports several classes of models, including Markov chains, HMM, context-free grammars, PROSITE patterns and more.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Y. Ponty, M. Termier and A. Denise [pdf] [bib]
GenRGenS: Software for generating random genomic sequences and structures
Bioinformatics, June 2006 22(12):1534-1535.
:: DESCRIPTION
SBSPKS is a webserver for carrying out sequence and structure based analysis of Polyketide Synthases, an important family of multifunctional megasynthases involved in the biosynthesis of a variety of pharmaceutically important secondary metabolites. The knowledge base for development of SBSPKS is derived from a comprehensive bioinformatics analysis of the sequence and structural features of a large number of experimentally characterized PKS gene clusters having known metabolic products and recently available crystal structures of PKS and FAS proteins.The interfaces for carrying out various tasks by SBSPKS are organized as three major functional units, namely NRPS_PKS, Model_3D_PKS and Dock_Dom_Anal .
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W487-96. Epub 2010 May 5.
SBSPKS: structure based sequence analysis of polyketide synthases.
Anand S, Prasad MV, Yadav G, Kumar N, Shehara J, Ansari MZ, Mohanty D.
:: DESCRIPTION
FCP is a publicly accessible web tool dedicated to analysing the current state and trends on the population of available structures along the classification schemes of enzymes (specially kinases and proteases), G protein-coupled receptors, nuclear receptors and transporters/channels, offering both graphical and quantitative data on the degree of functional coverage in that portion of the proteome by existing structures, as well as on the bias observed in the distribution of those structures among proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
FCP: functional coverage of the proteome by structures.
García-Serna R, Opatowski L, Mestres J.
Bioinformatics. 2006 Jul 15;22(14):1792-3. Epub 2006 May 16.
