:: 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
AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms. One major advantage over many other programs is that it is easy to introduce non-standard polymer linkages, unusual ligands or non-standard residues. Adding missing hydrogen atoms and completing partial structures, which are difficult for many programs, are straightforward in AMMP.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Protein Eng. 1999 Jun;12(6):469-74.
Molecular mechanics analysis of drug-resistant mutants of HIV protease.
Weber IT, Harrison RW.
:: DESCRIPTION
SloppyCell is a software environment for simulation and analysis of biomolecular networks.
::DEVELOPER
Ryan Gutenkunst while in the groups of Jim Sethna and Chris Myers at Cornell University.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Christopher R. Myers, Ryan N. Gutenkunst, James P. Sethna
“Python unleashed on systems biology”
Computing in Science and Engineering 9:34 (2007);
:: DESCRIPTION
Bodil is a modular, multi-platform software package for biomolecular visualization and modeling. Bodil aims to provide easy three-dimensional molecular graphics closely integrated with sequence viewing and sequence alignment editing. Functionality of Bodil is implemented in dynamically loaded modules. Most of the modules available in the present release provide visualization tools, with protein modeling, small-molecule ligand docking and other modules being currently under development. New modules can easily be added via a documented C++ application programming interface.
::DEVELOPER
Structural Bioinformatics Laboratory
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Lehtonen JV, Still DJ, Rantanen VV, Ekholm J, Björklund D, Iftikhar Z, Huhtala M, Repo S, Jussila A, Jaakkola J, Pentikäinen O, Nyrönen T, Salminen T, Gyllenberg M and Johnson M.
BODIL: a molecular modeling environment for structure-function analysis and drug design.
J Comput Aided Mol Des 2004 Jun;18(6):401-419.
:: DESCRIPTION
REvolver is a program to simulate protein sequence evolution. REvolver automatically integrates domain information described by a profile Hidden Markov Model (pHMM) into the simulation.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Tina Koestler, Arndt von Haeseler, and Ingo Ebersberger (2012)
REvolver: Modeling sequence evolution under domain constraints.
Mol Biol Evol (2012)doi: 10.1093/molbev/mss078
:: DESCRIPTION
PrISM (Protein Informatics System for Modeling) is an integrated computational system where computational tools are implemented for protein sequence and structure analysis and modeling.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Proteins. 1999;Suppl 3:66-72.
Sequence to structure alignment in comparative modeling using PrISM.
Yang AS, Honig B.
:: DESCRIPTION
Jackal is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package nest. JACKAL has the following capabilities: 1) comparative modeling based on single, composite or multiple templates; 2) side-chain prediction; 3) modeling residue mutation, insertion or deletion; 4) loop prediction; 5) structure refinement; 6) reconstruction of protein missing atoms;7) reconstruction of protein missing residues; 8) prediction of hydrogen atoms; 9) fast calculation of solvent accessible surface area; 10) structure superimposition.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
RD is intended to implement a program for statistical estimation of isoform expression levels using RNA-Seq based on the modeling of RNA degradation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wan L, Yan XT, Chen T and Sun FZ (2011)
RD: A Program for Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
submitted.
:: DESCRIPTION
The PNK (Petri Net Kernel) 2e is a software environment for the modeling and simulation of biological processes. It was developed as part of a M.Sc. project at the University of Edinburgh, UK. The software uses Stochastic Petri Nets (SPNs), a graphical representation of Markov Jump Processes.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
JigCell is a modeling and simulation software that also enable parameter estimation.The goal of this project is to support building and testing models for studying complex biochemical regulatory systems in general, and the cell cycle control system in particular.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Vass, M., N Allen, C.A. Shaffer, N. Ramakrishnan, L.T. Watson, and J.J. Tyson,
The JigCell Model Builder and Run Manager,
Bioinformatics 20, 18(2004), 3680-3681.
