simbTUM allows to define ODE-models or stochastic compartemental models of biological processes, to simulate, to fit data and to do some statistics (fitting and statistics for deterministic models only).
jagn is a software for an Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data, which can be used by computational methods to recover the network topology, and then, analyse the results based on complex networks measurements/topology.
Sunflower is an evolutionary model for promoters, analogous to the commonly used synonymous/nonsynonymous mutation models for protein-coding sequences.
HAPMIXMAP is a program for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program developed by Scheet and Stephens (2006). The program models unphased genotype data on unrelated individuals, and fits a model in which linkage disequilibrium is generated by K independent Poisson arrival processes corresponding to K modal haplotype states. This corresponds to the observation that typically 2-4 common haplotypes account for most of the allelic diversity in any haplotype block, and that rarer haplotypes are typically slight variants of these modal haplotypes. The block-like structure of haplotypes in the genome, corresponding to ancestral recombination hotspots, is modelled by allowing the arrival rate to vary across the genome.
phylolm is an R package providing a function for fitting phylogenetic linear regression models. The likelihood is calculated with an algorithm that is linear in the number of tips in the tree. The package also provides a function for simulating continuous traits along the tree.
FiltRest3D is a software for scoring and ranking of models according to their agreement with user-defined restraints.Automatic methods for protein structure prediction (fold-recognition, de novo folding, and docking programs) produce large sets of alternative models. These large model sets often include many native-like structures, which are scored as high as false positives. Such native-like models can be more easily identified based on data from experimental analyses used as structural restraints (e.g. identification of nearby residues by crosslinking, chemical modification, site-directed mutagenesis, deuterium exchange coupled with mass spectrometry etc.)
SMOG is a versatile software package for generating structure-based models.SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD.
de Oliveira AB Jr, Contessoto VG, Hassan A, Byju S, Wang A, Wang Y, Dodero-Rojas E, Mohanty U, Noel JK, Onuchic JN, Whitford PC. SMOG 2 and OpenSMOG: Extending the limits of structure-based models.
Protein Sci. 2021 Oct 16. doi: 10.1002/pro.4209. Epub ahead of print. PMID: 34655449.
Cromwell is an implementation of our algorithms for low-level processing of mass spectrometry proteomics data. Cromwell represents our third attempt (at least) to find a method to process spectra that both works quickly and achieves reasonably good results.