conStruct v1.0.3 – Modeling Continuous and Discrete Population Genetic Structure

conStruct v1.0.3

:: DESCRIPTION

conStruct (continuous Structure) is a statistical tool for modeling continuous and discrete population genetic structure.

::DEVELOPER

the Bradburd Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R package

:: DOWNLOAD

conStruct

:: MORE INFORMATION

Citation

Bradburd GS, Coop GM, Ralph PL.
Inferring Continuous and Discrete Population Genetic Structure Across Space.
Genetics. 2018 Sep;210(1):33-52. doi: 10.1534/genetics.118.301333. Epub 2018 Jul 19. PMID: 30026187; PMCID: PMC6116973.

ModeRNA 1.7.1 – Comparative RNA 3D Modeling

ModeRNA 1.7.1

:: DESCRIPTION

ModeRNA is a program for comparative modeling of RNA 3D structures. It requires a pairwise sequence alignment and a structural template to generate a 3D structural model of the target RNA sequence via either a fully automated or script-based approaches. ModeRNA is capable of handling 115 different nucleotide modifications and bridging gaps using fragments derived from an extensive fragment library.

::DEVELOPER

Bujnicki Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

ModeRNA

:: MORE INFORMATION

Citation

Magdalena Rother, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki
ModeRNA: a tool for comparative modeling of RNA 3D structure
Nucl. Acids Res.(2011)doi: 10.1093

CAMer – R package for Continuous Admixture Modeling

CAMer

:: DESCRIPTION

CAMer package is a R package for inferring continuous admixture time interval, which is based on the result of iMAAPs.

::DEVELOPER

Population Genomics Group (PGG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

CAMer

:: MORE INFORMATION

Citation

Zhou Y, Qiu H, Xu S.
Modeling Continuous Admixture Using Admixture-Induced Linkage Disequilibrium.
Sci Rep. 2017 Feb 23;7:43054. doi: 10.1038/srep43054. PMID: 28230170; PMCID: PMC5322361.

MODELLER 10.1 – Comparative Protein Structure Modeling

MODELLER 10.1

:: DESCRIPTION

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

  MODELLER

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1137:1-15. doi: 10.1007/978-1-4939-0366-5_1.
Protein structure modeling with MODELLER.
Webb B1, Sali A.

N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali.
Comparative Protein Structure Modeling With MODELLER.
Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.

iMADS 1.0.3 – integrative Modeling and Analysis of Differential Specificity

iMADS 1.0.3

:: DESCRIPTION

iMADS is a combined computational-experimental strategy to identify and study the differences in DNA-binding specificity between transcription factor (TF) family members, i.e. paralogous TFs.

::DEVELOPER

The Gordan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

iMADS

:: MORE INFORMATION

Citation:

Shen N, Zhao J, Schipper JL, Zhang Y, Bepler T, Leehr D, Bradley J, Horton J, Lapp H, Gordan R.
Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding.
Cell Syst. 2018 Apr 25;6(4):470-483.e8. doi: 10.1016/j.cels.2018.02.009. Epub 2018 Mar 28. PMID: 29605182; PMCID: PMC6008103.

TASSER-Lite 1.0 – Protein Structure Modeling tool

TASSER-Lite 1.0

:: DESCRIPTION

TASSER-Lite is a protein structure comparative modeling tool. It is limited to protein target-template pairs whose pairwise sequence identity is >25% to the best threading template. It is optimized to model single domain proteins whose lengths range from 41-200 residues.

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TASSER-Lite

:: MORE INFORMATION

Citation

Pandit, S B, Zhang Y, Skolnick J. 2006.
TASSER-Lite: an automated tool for protein comparative modeling.
Biophysical journal. 91(11):4180-90.

RW 1.0 – Protein Structure Modeling and Structure Decoy Recognition

RW 1.0

:: DESCRIPTION

RW (Random-Walk) is distance-dependent atomic potential for protein structure modeling and structure decoy recognition. It was derived from 1,383 high-resolution PDB structures using an ideal random-walk chain as the reference state. The RW potential has been extensively optimized and tested on a variety of protein structure decoy sets and demonstrates a significant power in protein structure recognition and a strong correlation with the RMSD of decoys to the native structures

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 calRW

:: MORE INFORMATION

Citation

Zhang J, Zhang Y (2010)
A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction.
PLoS ONE 5(10): e15386.

BDTree 1.01 – Modeling of Gene Expression Regulation

BDTree 1.01

:: DESCRIPTION

BDTree is a Bi-dimensional Regression Tree approach for modeling transcriptional regulation

::DEVELOPER

Jianhua Ruan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  •  Java

:: DOWNLOAD

  BDTree

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Feb 1;22(3):332-40. Epub 2005 Nov 22.
A bi-dimensional regression tree approach to the modeling of gene expression regulation.
Ruan J, Zhang W.

GOMoDo beta – GPCR Online MOdeling and DOcking server

GOMoDo beta

:: DESCRIPTION

GOMoDo (GPCR Online Modeling and Docking) is a web server to seamlessly model GPCR (G-protein coupled receptors ) structures and dock ligands to the models in a single consistent pipeline.

::DEVELOPER

Department of Biotechnology, University of Verona | Institute of Computational Biomedicine (INM-9/IAS-5), Forschungszentrum Jülich.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Sandal M, Duy TP, Cona M, Zung H, Carloni P, et al. (2013)
GOMoDo: A GPCRs Online Modeling and Docking Webserver.
PLoS ONE 8(9): e74092. doi:10.1371/journal.pone.0074092

BRAGI 20091106 – A Protein Visualization and Modeling Program

BRAGI 20091106

:: DESCRIPTION

BRAGI is a well-established package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules.BRAGI enables you to view and explore the three-dimensional (3D) structure of any macromolecule. You can explore proteins, DNA, RNA, carbohydrates, and complexes, such as between transcriptional regulatory proteins and DNA, or enzymes and drugs.

::DEVELOPER

BRAGI Team

:: SCREENSHOTS

BRAGI

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 BRAGI

:: MORE INFORMATION

Citation

BRAGI: linking and visualization of database information in a 3D viewer and modeling tool.
Reichelt J, Dieterich G, Kvesic M, Schomburg D, Heinz DW.
Bioinformatics. 2005 Apr 1;21(7):1291-3. Epub 2004 Nov 16.