PlantPAN 2.0 – Identifying Combinatorial Cis-regulatory Elements with Distance Constraint in Plant Gene Groups

PlantPAN 2.0

:: DESCRIPTION

PlantPAN (Plant Promoter Analysis Navigator) is a database-assisted system for recognizing combinatorial cis-regulatory elements with distance constraint in plant co-expressed genes.

::DEVELOPER

Integrative System Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants.
Chow CN, Zheng HQ, Wu NY, Chien CH, Huang HD, Lee TY, Chiang-Hsieh YF, Hou PF, Yang TY, Chang WC.
Nucleic Acids Res. 2015 Oct 17. pii: gkv1035.

BMC Genomics. 2008 Nov 26;9:561. doi: 10.1186/1471-2164-9-561.
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups.
Chang WC, Lee TY, Huang HD, Huang HY, Pan RL.

Concoord 2.1.2 – Protein Structure Generation from Distance Constraint

Concoord 2.1.2

:: DESCRIPTION

CONCOORD is a method to generate protein conformations around a known structure based on geometric 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.

::DEVELOPER

Bert de Groot

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Concoord

:: MORE INFORMATION

Citation

B.L. de Groot, D.M.F. van Aalten, R.M. Scheek, A. Amadei, G. Vriend and H.J.C. Berendsen;
Prediction of protein conformational freedom from distance constraints“,
Proteins 29: 240-251 (1997)