Bujnicki JM - Search Results

1

RNA target highlights in CASP15: Evaluation of predicted models by structure providers.

Kretsch RC, Andersen ES, Bujnicki JM, Chiu W, Das R, Luo B, Masquida B, McRae EKS, Schroeder GM, Su Z, Wedekind JE, Xu L, Zhang K, Zheludev IN, Moult J, Kryshtafovych A. Kretsch RC, et al. Among authors: bujnicki jm. Proteins. 2023 Dec;91(12):1600-1615. doi: 10.1002/prot.26550. Epub 2023 Jul 19. Proteins. 2023. PMID: 37466021

2

LiveBench-2: large-scale automated evaluation of protein structure prediction servers.

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. Bujnicki JM, et al. Proteins. 2001;Suppl 5:184-91. doi: 10.1002/prot.10039. Proteins. 2001. PMID: 11835496

3

A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation.

Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM. Kosinski J, et al. Among authors: bujnicki jm. Proteins. 2003;53 Suppl 6:369-79. doi: 10.1002/prot.10545. Proteins. 2003. PMID: 14579325

4

Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface.

Radlinska M, Kondrzycka-Dada A, Piekarowicz A, Bujnicki JM. Radlinska M, et al. Among authors: bujnicki jm. Proteins. 2005 Feb 1;58(2):263-70. doi: 10.1002/prot.20297. Proteins. 2005. PMID: 15558546

5

Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.

Koliński A, Bujnicki JM. Koliński A, et al. Among authors: bujnicki jm. Proteins. 2005;61 Suppl 7:84-90. doi: 10.1002/prot.20723. Proteins. 2005. PMID: 16187348

6

FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.

Kosinski J, Gajda MJ, Cymerman IA, Kurowski MA, Pawlowski M, Boniecki M, Obarska A, Papaj G, Sroczynska-Obuchowicz P, Tkaczuk KL, Sniezynska P, Sasin JM, Augustyn A, Bujnicki JM, Feder M. Kosinski J, et al. Among authors: bujnicki jm. Proteins. 2005;61 Suppl 7:106-113. doi: 10.1002/prot.20726. Proteins. 2005. PMID: 16187351

7

Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.

Skowronek KJ, Kosinski J, Bujnicki JM. Skowronek KJ, et al. Among authors: bujnicki jm. Proteins. 2006 Jun 1;63(4):1059-68. doi: 10.1002/prot.20920. Proteins. 2006. PMID: 16498623

8

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.

Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'Amaré AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E. Miao Z, et al. Among authors: bujnicki jm. RNA. 2015 Jun;21(6):1066-84. doi: 10.1261/rna.049502.114. Epub 2015 Apr 16. RNA. 2015. PMID: 25883046 Free PMC article.

9

RNA 3D structure prediction guided by independent folding of homologous sequences.

Magnus M, Kappel K, Das R, Bujnicki JM. Magnus M, et al. Among authors: bujnicki jm. BMC Bioinformatics. 2019 Oct 22;20(1):512. doi: 10.1186/s12859-019-3120-y. BMC Bioinformatics. 2019. PMID: 31640563 Free PMC article.

10

RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints.

Baulin EF, Mukherjee S, Moafinejad SN, Wirecki TK, Badepally NG, Jaryani F, Stefaniak F, Amiri Farsani M, Ray A, Rocha de Moura T, Bujnicki JM. Baulin EF, et al. Among authors: bujnicki jm. Proteins. 2023 Dec;91(12):1800-1810. doi: 10.1002/prot.26575. Epub 2023 Aug 25. Proteins. 2023. PMID: 37622458

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