Methods & Software

Go to my GitHub page.

You can follow the source code of the released methods and software from my GitHub source management account. Press the Git logo at the right side to go to the page. You are welcome to report any possible issues, bugs or feature requests through the GitHub interface. Most of the released source code is free under the GPL2 public license terms.

In case you use one of the programs listed below, and would like to make a small donation to support my research and the continuous development of open source tools, please use the following button (common cards and/or PayPal). Your name will appear in the dedicated list of sponsors listed here and in each program separately. Thank you very much!

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A number of advanced computational biology tools: TrantoRStarCoreQuadRand; Optimus and Conqueror are coming soon.



Quadron logo

Quadron is a program to calculate the sequence-driven DNA G-quadruplex formation propensities in DNA sequences and whole genomes. The calculations are based on a model obtained via a large-scale machine learning from experimental G4-seq dataset. The program, user manual and source code can be accessed through here.


trek logo

Trek is a program to calculate the germline context-dependent core mutation rate constants in the human genome. The calculations are based on the transposon exposed mutation rates as described in the referred publication. The database, mapper program, server application manual and source code can be accessed through here.


http://www-sidechain.ch.cam.ac.uk/CH3Shift/

CH3Shift is a structure-based predictor of proton chemical shifts of protein side-chain methyl groups. CH3Shift is available both in a stand-alone and server implementations via the following link. The manual can be accessed from the same url. The source code is here.


http://www-sidechain.ch.cam.ac.uk/ArShift/

ArShift is a structure-based predictor of proton chemical shifts of aromatic side-chains. ArShift is available both in a stand-alone and server implementations via the following link. The manual can be accessed from the same url. The source code is here.


na

RingPar is a web server for exploring fittings of different electric field and ring current model combinations against the calculated change is chemical shifts and chemical shift anisotropies imposed by neighbouring conjugated systems in nucleic acid bases. The server (manual is coming soon) is accessable through this link. The source code is here.


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RingCurrent is a utility code provided in both R and Fortran95+ languages to calculate the ring current geometric parameters (Pople and Haigh-Mallion) at the point specified near a conjugated ring, where the Cartesian coordinates of both the query point and the positions of the ring atoms (5- or 6-membered) are supplied. The source code is here.


GaussMD logo

GaussMD is a utility code to extract geometric information, structures, and plots out of ab initio molecular dynamics simulation outputs of Gaussian0X. GaussMD uses a highly versatile input that allows users to flexibly define data types needed for extraction or calculation out of the supplied trajectory file. The source code is here.


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