a useful database by Hoffmann et al. (Max Planck Institute for Polymer Research) containing trajectories from 15,120 MD simulations of small-molecule drugs permeating across a phospholipid membrane.


  • C. Hoffmann, A. Centi, R. Menichetti, and T. Bereau, "Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations", Scientific Data, vol. 7, 2020. http://dx.doi.org/10.1038/s41597-020-0391-0
  • The three most common classes of kinase inhibitors are Type I, Type I.5, and Type II. In a Guest Post, Cyril Bucher has a nice graphic summarizing illustrating these, and highlights an excellent recent paper by Filip Miljković, Raquel Rodríguez Pérez, and Jurgen Bajorath describing machine-learning approaches for computationally predicting inhibitor binding modes.



    [abstract] Fungi are an understudied, biotechnologically valuable group of organisms. Due to the immense range of habitats that fungi inhabit, and the consequent need to compete against a diverse array of other fungi, bacteria, and animals, fungi have developed numerous survival mechanisms. The unique attributes of fungi thus herald great promise for their application in biotechnology and industry. Moreover, fungi can be grown with relative ease, making production at scale viable. The search for fungal biodiversity, and the construction of a living fungi collection, both have incredible economic potential in locating organisms with novel industrial uses that will lead to novel products. This manuscript reviews fifty ways in which fungi can potentially be utilized as biotechnology. We provide notes and examples for each potential exploitation and give examples from our own work and the work of other notable researchers. We also provide a flow chart that can be used to convince funding bodies of the importance of fungi for biotechnological research and as potential products. Fungi have provided the world with penicillin, lovastatin, and other globally significant medicines, and they remain an untapped resource with enormous industrial potential.

  • K.D. Hyde, J. Xu, S. Rapior, R. Jeewon, S. Lumyong, A.G.T. Niego, P.D. Abeywickrama, J.V.S. Aluthmuhandiram, R.S. Brahamanage, S. Brooks, A. Chaiyasen, K.W.T. Chethana, P. Chomnunti, C. Chepkirui, B. Chuankid, N.I. de Silva, M. Doilom, C. Faulds, E. Gentekaki, V. Gopalan, P. Kakumyan, D. Harishchandra, H. Hemachandran, S. Hongsanan, A. Karunarathna, S.C. Karunarathna, S. Khan, J. Kumla, R.S. Jayawardena, J. Liu, N. Liu, T. Luangharn, A.P.G. Macabeo, D.S. Marasinghe, D. Meeks, P.E. Mortimer, P. Mueller, S. Nadir, K.N. Nataraja, S. Nontachaiyapoom, M. O’Brien, W. Penkhrue, C. Phukhamsakda, U.S. Ramanan, A.R. Rathnayaka, R.B. Sadaba, B. Sandargo, B.C. Samarakoon, D.S. Tennakoon, R. Siva, W. Sriprom, T.S. Suryanarayanan, K. Sujarit, N. Suwannarach, T. Suwunwong, B. Thongbai, N. Thongklang, D. Wei, S.N. Wijesinghe, J. Winiski, J. Yan, E. Yasanthika, and M. Stadler, "The amazing potential of fungi: 50 ways we can exploit fungi industrially", Fungal Diversity, vol. 97, pp. 1-136, 2019. http://dx.doi.org/10.1007/s13225-019-00430-9