Funding statement
Financial support from Vetenskapsrådet (2019-01403) and Swedish Cancer
Society (CAN 2017/699) is gratefully acknowledged.
References
Aderinwale, T., Christoffer, C.W., Sarkar, D., Alnabati, E., and Kihara,
D. (2020). Computational structure modeling for diverse categories of
macromolecular interactions. Curr Opin Struct Biol 64 , 1-8.
Baker, M. (2016). 1,500 scientists lift the lid on reproducibility.
Nature 533 , 452-454.
Begley, C.G., and Ioannidis, J.P. (2015). Reproducibility in science:
improving the standard for basic and preclinical research. Circ Res116 , 116-126.
Bienert, S., Waterhouse, A., de Beer, T.A., Tauriello, G., Studer, G.,
Bordoli, L., and Schwede, T. (2017). The SWISS-MODEL Repository-new
features and functionality. Nucleic acids research 45 , D313-d319.
Brooks, B.R., Brooks, C.L., 3rd, Mackerell, A.D., Jr., Nilsson, L.,
Petrella, R.J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch,
S., et al. (2009). CHARMM: the biomolecular simulation program. J
Comput Chem 30 , 1545-1614.
Dalgleish, R., Flicek, P., Cunningham, F., Astashyn, A., Tully, R.E.,
Proctor, G., Chen, Y., McLaren, W.M., Larsson, P., Vaughan, B.W.,
et al. (2010). Locus Reference Genomic sequences: an improved basis for
describing human DNA variants. Genome Med 2 , 24.
den Dunnen, J.T., and Antonarakis, S.E. (2001). Nomenclature for the
description of human sequence variations. Hum Genet 109 , 121-124.
Dhingra, S., Sowdhamini, R., Cadet, F., and Offmann, B. (2020). A glance
into the evolution of template-free protein structure prediction
methodologies. Biochimie 175 , 85-92.
Dorn, M., MB, E.S., Buriol, L.S., and Lamb, L.C. (2014).
Three-dimensional protein structure prediction: Methods and
computational strategies. Comput Biol Chem 53pb , 251-276.
Gonnet, G.H., Cohen, M.A., and Benner, S.A. (1994). Analysis of amino
acid substitution during divergent evolution: the 400 by 400 dipeptide
substitution matrix. Biochem Biophys Res Commun 199 , 489-496.
Gray, K.A., Yates, B., Seal, R.L., Wright, M.W., and Bruford, E.A.
(2015). Genenames.org: the HGNC resources in 2015. Nucleic acids
research 43 , D1079-1085.
Gund, P., Barry, D.C., Blaney, J.M., and Cohen, N.C. (1988). Guidelines
for publications in molecular modeling related to medicinal chemistry. J
Med Chem 31 , 2230-2234.
Haddad, Y., Adam, V., and Heger, Z. (2020). Ten quick tips for homology
modeling of high-resolution protein 3D structures. PLoS computational
biology 16 , e1007449.
Hooft, R.W., Vriend, G., Sander, C., and Abola, E.E. (1996). Errors in
protein structures. Nature 381 , 272.
Iqbal, S.A., Wallach, J.D., Khoury, M.J., Schully, S.D., and Ioannidis,
J.P. (2016). Reproducible Research Practices and Transparency across the
Biomedical Literature. PLoS biology 14 , e1002333.
Johnson, G.T., and Hertig, S. (2014). A guide to the visual analysis and
communication of biomolecular structural data. Nat Rev Mol Cell Biol15 , 690-698.
Kc, D.B. (2017). Recent advances in sequence-based protein structure
prediction. Briefings in bioinformatics 18 , 1021-1032.
Khan, S., and Vihinen, M. (2009). Evaluation of accuracy and
applicability of protein models: retrospective analysis of biological
and biomedical predictions. In Silico Biol 9 , 307-331.
Kuhlman, B., and Bradley, P. (2019). Advances in protein structure
prediction and design. Nat Rev Mol Cell Biol 20 , 681-697.
Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. (1993).
PROCHECK: a program to check the stereochemical quality of protein
structures. J Appl Cryst 26 , 283-291.
Lüthy, R., Bowie, J.U., and Eisenberg, D. (1992). Assessment of protein
models with three-dimensional profiles. Nature 356 , 83-85.
Martí-Renom, M.A., Stuart, A.C., Fiser, A., Sánchez, R., Melo, F., and
Sali, A. (2000). Comparative protein structure modeling of genes and
genomes. Annu Rev Biophys Biomol Struct 29 , 291-325.
Mura, C., McCrimmon, C.M., Vertrees, J., and Sawaya, M.R. (2010). An
introduction to biomolecular graphics. PLoS computational biology6 .
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt,
D.M., Meng, E.C., and Ferrin, T.E. (2004). UCSF Chimera–a
visualization system for exploratory research and analysis. J Comput
Chem 25 , 1605-1612.
Pieper, U., Webb, B.M., Dong, G.Q., Schneidman-Duhovny, D., Fan, H.,
Kim, S.J., Khuri, N., Spill, Y.G., Weinkam, P., Hammel, M., et
al. (2014). ModBase, a database of annotated comparative protein
structure models and associated resources. Nucleic acids research42 , D336-346.
Ramachandran, G.N., Ramakrishnan, C., and Sasisekharan, V. (1963).
Stereochemistry of polypeptide chain configurations. Journal of
molecular biology 7 , 95-99.
Sarkans, U., Gostev, M., Athar, A., Behrangi, E., Melnichuk, O., Ali,
A., Minguet, J., Rada, J.C., Snow, C., Tikhonov, A., et al.(2018). The BioStudies database-one stop shop for all data supporting a
life sciences study. Nucleic acids research 46 , D1266-d1270.
Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H.M., Jones, D.,
Brenner, S.E., Burley, S.K., Das, R., Dokholyan, N.V., et al.(2009). Outcome of a workshop on applications of protein models in
biomedical research. Structure 17 , 151-159.
Shapovalov, M.V., and Dunbrack, R.L., Jr. (2011). A smoothed
backbone-dependent rotamer library for proteins derived from adaptive
kernel density estimates and regressions. Structure 19 , 844-858.
Shen, M.Y., and Sali, A. (2006). Statistical potential for assessment
and prediction of protein structures. Protein science : a publication of
the Protein Society 15 , 2507-2524.
Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W.,
Lopez, R., McWilliam, H., Remmert, M., Söding, J., et al. (2011).
Fast, scalable generation of high-quality protein multiple sequence
alignments using Clustal Omega. Molecular systems biology 7 , 539.
Tan, T.W., Tong, J.C., Khan, A.M., de Silva, M., Lim, K.S., and
Ranganathan, S. (2010). Advancing standards for bioinformatics
activities: persistence, reproducibility, disambiguation and Minimum
Information About a Bioinformatics investigation (MIABi). BMC Genomics11 Suppl 4 , S27.
Vihinen, M. (2012). How to evaluate performance of prediction methods?
Measures and their interpretation in variation effect analysis. BMC
Genomics 13 Suppl 4 , S2.
Vihinen, M. (2013). Guidelines for reporting and using prediction tools
for genetic variation analysis. Human mutation 34 , 275-282.
Vihinen, M. (2014). Variation Ontology for annotation of variation
effects and mechanisms. Genome research 24 , 356-364.
Vihinen, M. (2020). Guidelines for systematic reporting of sequence
alignments. Biol Meth Protoc bpaa001 .
Williams, C.J., Headd, J.J., Moriarty, N.W., Prisant, M.G., Videau,
L.L., Deis, L.N., Verma, V., Keedy, D.A., Hintze, B.J., Chen,
V.B., et al. (2018). MolProbity: More and better reference data
for improved all-atom structure validation. Protein science : a
publication of the Protein Society 27 , 293-315.