Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 216

1.

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing.

Honorato RV, Roel-Touris J, Bonvin AMJJ.

Front Mol Biosci. 2019 Oct 1;6:102. doi: 10.3389/fmolb.2019.00102. eCollection 2019.

2.

Computational approaches to therapeutic antibody design: established methods and emerging trends.

Norman RA, Ambrosetti F, Bonvin AMJJ, Colwell LJ, Kelm S, Kumar S, Krawczyk K.

Brief Bioinform. 2019 Oct 18. pii: bbz095. doi: 10.1093/bib/bbz095. [Epub ahead of print]

PMID:
31626279
3.

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.

Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ.

Proteins. 2019 Oct 14. doi: 10.1002/prot.25838. [Epub ahead of print]

PMID:
31612567
4.

Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK.

Roel-Touris J, Don CG, V Honorato R, Rodrigues JPGLM, Bonvin AMJJ.

J Chem Theory Comput. 2019 Oct 10. doi: 10.1021/acs.jctc.9b00310. [Epub ahead of print]

PMID:
31539250
5.

Sharing Data from Molecular Simulations.

Abraham M, Apostolov R, Barnoud J, Bauer P, Blau C, Bonvin AMJJ, Chavent M, Chodera J, Čondić-Jurkić K, Delemotte L, Grubmüller H, Howard RJ, Jordan EJ, Lindahl E, Ollila OHS, Selent J, Smith DGA, Stansfeld PJ, Tiemann JKS, Trellet M, Woods C, Zhmurov A.

J Chem Inf Model. 2019 Oct 28;59(10):4093-4099. doi: 10.1021/acs.jcim.9b00665. Epub 2019 Oct 11.

PMID:
31525920
6.

The structural details of the interaction of single-stranded DNA binding protein hSSB2 (NABP1/OBFC2A) with UV-damaged DNA.

Lawson T, El-Kamand S, Boucher D, Duong DC, Kariawasam R, Bonvin AMJJ, Richard DJ, Gamsjaeger R, Cubeddu L.

Proteins. 2019 Aug 23. doi: 10.1002/prot.25806. [Epub ahead of print]

PMID:
31443132
7.

Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems.

Kurkcuoglu Z, Bonvin AMJJ.

Proteins. 2019 Aug 22. doi: 10.1002/prot.25802. [Epub ahead of print]

PMID:
31441121
8.

Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase.

Goldbach L, Vermeulen BJA, Caner S, Liu M, Tysoe C, van Gijzel L, Yoshisada R, Trellet M, van Ingen H, Brayer GD, Bonvin AMJJ, Jongkees SAK.

ACS Chem Biol. 2019 Aug 16;14(8):1751-1759. doi: 10.1021/acschembio.9b00290. Epub 2019 Jul 19.

9.

iScore: A novel graph kernel-based function for scoring protein-protein docking models.

Geng C, Jung Y, Renaud N, Honavar V, Bonvin AMJJ, Xue LC.

Bioinformatics. 2019 Jun 14. pii: btz496. doi: 10.1093/bioinformatics/btz496. [Epub ahead of print]

PMID:
31199455
10.

PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes.

Jiménez-García B, Elez K, Koukos PI, Bonvin AMJJ, Vangone A.

Bioinformatics. 2019 May 29. pii: btz437. doi: 10.1093/bioinformatics/btz437. [Epub ahead of print]

PMID:
31141126
11.

Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server.

Vangone A, Schaarschmidt J, Koukos P, Geng C, Citro N, Trellet ME, Xue LC, Bonvin AMJJ.

Bioinformatics. 2019 May 1;35(9):1585-1587. doi: 10.1093/bioinformatics/bty816.

PMID:
31051038
12.

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape.

Basciu A, Malloci G, Pietrucci F, Bonvin AMJJ, Vargiu AV.

J Chem Inf Model. 2019 Apr 22;59(4):1515-1528. doi: 10.1021/acs.jcim.8b00730. Epub 2019 Mar 28.

PMID:
30883122
13.

pdb-tools: a swiss army knife for molecular structures.

Rodrigues JPGLM, Teixeira JMC, Trellet M, Bonvin AMJJ.

F1000Res. 2018 Dec 20;7:1961. doi: 10.12688/f1000research.17456.1. eCollection 2018.

14.

Natural helix 9 mutants of PPARγ differently affect its transcriptional activity.

Broekema MF, Massink MPG, Donato C, de Ligt J, Schaarschmidt J, Borgman A, Schooneman MG, Melchers D, Gerding MN, Houtman R, Bonvin AMJJ, Majithia AR, Monajemi H, van Haaften GW, Soeters MR, Kalkhoven E.

Mol Metab. 2019 Feb;20:115-127. doi: 10.1016/j.molmet.2018.12.005. Epub 2018 Dec 16.

15.

Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification.

Elez K, Bonvin AMJJ, Vangone A.

BMC Bioinformatics. 2018 Nov 30;19(Suppl 15):438. doi: 10.1186/s12859-018-2414-9.

16.

iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations.

Geng C, Vangone A, Folkers GE, Xue LC, Bonvin AMJJ.

Proteins. 2019 Feb;87(2):110-119. doi: 10.1002/prot.25630. Epub 2018 Dec 3.

17.

A Membrane Protein Complex Docking Benchmark.

Koukos PI, Faro I, van Noort CW, Bonvin AMJJ.

J Mol Biol. 2018 Dec 7;430(24):5246-5256. doi: 10.1016/j.jmb.2018.11.005. Epub 2018 Nov 9.

18.

Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis.

Roseboom W, Nazir MG, Meiresonne NY, Mohammadi T, Verheul J, Buncherd H, Bonvin AMJJ, de Koning LJ, de Koster CG, de Jong L, den Blaauwen T.

Int J Mol Sci. 2018 Sep 26;19(10). pii: E2928. doi: 10.3390/ijms19102928.

19.

Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3.

Koukos PI, Xue LC, Bonvin AMJJ.

J Comput Aided Mol Des. 2019 Jan;33(1):83-91. doi: 10.1007/s10822-018-0148-4. Epub 2018 Aug 20.

20.

Defining distance restraints in HADDOCK.

Bonvin AMJJ, Karaca E, Kastritis PL, Rodrigues JPGLM.

Nat Protoc. 2018 Jul;13(7):1503. doi: 10.1038/s41596-018-0017-6. Epub 2018 Jun 25. No abstract available.

PMID:
29942005
21.

Rapid Prediction of Multi-dimensional NMR Data Sets Using FANDAS.

Narasimhan S, Mance D, Pinto C, Weingarth M, Bonvin AMJJ, Baldus M.

Methods Mol Biol. 2018;1688:111-132. doi: 10.1007/978-1-4939-7386-6_6.

PMID:
29151207
22.

Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age.

Schaarschmidt J, Monastyrskyy B, Kryshtafovych A, Bonvin AMJJ.

Proteins. 2018 Mar;86 Suppl 1:51-66. doi: 10.1002/prot.25407. Epub 2017 Nov 7.

23.

Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.

Kurkcuoglu Z, Koukos PI, Citro N, Trellet ME, Rodrigues JPGLM, Moreira IS, Roel-Touris J, Melquiond ASJ, Geng C, Schaarschmidt J, Xue LC, Vangone A, Bonvin AMJJ.

J Comput Aided Mol Des. 2018 Jan;32(1):175-185. doi: 10.1007/s10822-017-0049-y. Epub 2017 Aug 22.

24.

SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots.

Moreira IS, Koukos PI, Melo R, Almeida JG, Preto AJ, Schaarschmidt J, Trellet M, Gümüş ZH, Costa J, Bonvin AMJJ.

Sci Rep. 2017 Aug 14;7(1):8007. doi: 10.1038/s41598-017-08321-2.

25.

M3: an integrative framework for structure determination of molecular machines.

Karaca E, Rodrigues JPGLM, Graziadei A, Bonvin AMJJ, Carlomagno T.

Nat Methods. 2017 Sep;14(9):897-902. doi: 10.1038/nmeth.4392. Epub 2017 Aug 14.

PMID:
28805795
26.

Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418).

Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond ASJ, Visscher KM, Trellet M, Kastritis PL, Bonvin AMJJ.

Proteins. 2017 Aug;85(8):1589-1590. doi: 10.1002/prot.25339. No abstract available.

PMID:
28730688
27.

Membrane proteins structures: A review on computational modeling tools.

Almeida JG, Preto AJ, Koukos PI, Bonvin AMJJ, Moreira IS.

Biochim Biophys Acta Biomembr. 2017 Oct;1859(10):2021-2039. doi: 10.1016/j.bbamem.2017.07.008. Epub 2017 Jul 15. Review.

28.

Supramolecular Organization and Functional Implications of K+  Channel Clusters in Membranes.

Visscher KM, Medeiros-Silva J, Mance D, Rodrigues JPGLM, Daniëls M, Bonvin AMJJ, Baldus M, Weingarth M.

Angew Chem Int Ed Engl. 2017 Oct 16;56(43):13222-13227. doi: 10.1002/anie.201705723. Epub 2017 Aug 9.

29.

Correction: Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody.

de Bruin RCG, Stam AGM, Vangone A, van Bergen En Henegouwen PMP, Verheul HMW, Sebestyén Z, Kuball J, Bonvin AMJJ, de Gruijl TD, van der Vliet HJ.

J Immunol. 2017 May 1;198(9):3759. doi: 10.4049/jimmunol.1700317. No abstract available.

30.

Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK.

Geng C, Narasimhan S, Rodrigues JP, Bonvin AM.

Methods Mol Biol. 2017;1561:109-138. doi: 10.1007/978-1-4939-6798-8_8.

PMID:
28236236
31.

The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes.

van Zundert GC, Trellet M, Schaarschmidt J, Kurkcuoglu Z, David M, Verlato M, Rosato A, Bonvin AM.

J Mol Biol. 2017 Feb 3;429(3):399-407. doi: 10.1016/j.jmb.2016.11.032. Epub 2016 Dec 7.

32.

Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody.

de Bruin RC, Stam AG, Vangone A, van Bergen En Henegouwen PM, Verheul HM, Sebestyén Z, Kuball J, Bonvin AM, de Gruijl TD, van der Vliet HJ.

J Immunol. 2017 Jan 1;198(1):308-317. Epub 2016 Nov 28. Erratum in: J Immunol. 2017 May 1;198(9):3759.

33.

Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.

Felix J, Kandiah E, De Munck S, Bloch Y, van Zundert GC, Pauwels K, Dansercoer A, Novanska K, Read RJ, Bonvin AM, Vergauwen B, Verstraete K, Gutsche I, Savvides SN.

Nat Commun. 2016 Nov 7;7:13228. doi: 10.1038/ncomms13228.

34.

Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1.

Vangone A, Rodrigues JP, Xue LC, van Zundert GC, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond AS, Visscher KM, Trellet M, Kastritis PL, Bonvin AM.

Proteins. 2017 Mar;85(3):417-423. doi: 10.1002/prot.25198. Epub 2016 Nov 24. Erratum in: Proteins. 2017 Aug;85(8):1589-1590.

35.

Structure of the bacterial plant-ferredoxin receptor FusA.

Grinter R, Josts I, Mosbahi K, Roszak AW, Cogdell RJ, Bonvin AM, Milner JJ, Kelly SM, Byron O, Smith BO, Walker D.

Nat Commun. 2016 Oct 31;7:13308. doi: 10.1038/ncomms13308.

36.

dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking.

Spiliotopoulos D, Kastritis PL, Melquiond AS, Bonvin AM, Musco G, Rocchia W, Spitaleri A.

Front Mol Biosci. 2016 Aug 31;3:46. doi: 10.3389/fmolb.2016.00046. eCollection 2016.

37.

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.

Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A.

Bioinformatics. 2016 Dec 1;32(23):3676-3678. Epub 2016 Aug 8.

PMID:
27503228
38.

A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.

Melo R, Fieldhouse R, Melo A, Correia JD, Cordeiro MN, Gümüş ZH, Costa J, Bonvin AM, Moreira IS.

Int J Mol Sci. 2016 Jul 27;17(8). pii: E1215. doi: 10.3390/ijms17081215.

39.

Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids.

van Zundert GCP, Bonvin AMJJ.

J Struct Biol. 2016 Aug;195(2):252-258. doi: 10.1016/j.jsb.2016.06.011. Epub 2016 Jun 15.

PMID:
27318041
40.

Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes.

Geng C, Vangone A, Bonvin AMJJ.

Protein Eng Des Sel. 2016 Aug;29(8):291-299. doi: 10.1093/protein/gzw020. Epub 2016 Jun 9.

PMID:
27284087
41.

New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies.

Liu Y, Rodrigues JP, Bonvin AM, Zaal EA, Berkers CR, Heger M, Gawarecka K, Swiezewska E, Breukink E, Egmond MR.

J Biol Chem. 2016 Jul 15;291(29):15057-68. doi: 10.1074/jbc.M116.717884. Epub 2016 May 18.

42.

A benchmark testing ground for integrating homology modeling and protein docking.

Bohnuud T, Luo L, Wodak SJ, Bonvin AM, Weng Z, Vajda S, Schueler-Furman O, Kozakov D.

Proteins. 2017 Jan;85(1):10-16. doi: 10.1002/prot.25063. Epub 2016 Nov 13.

43.

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.

Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.

44.

Template-based protein-protein docking exploiting pairwise interfacial residue restraints.

Xue LC, Rodrigues JPGLM, Dobbs D, Honavar V, Bonvin AMJJ.

Brief Bioinform. 2017 May 1;18(3):458-466. doi: 10.1093/bib/bbw027.

45.

Data publication with the structural biology data grid supports live analysis.

Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P.

Nat Commun. 2016 Mar 7;7:10882. doi: 10.1038/ncomms10882.

46.

The solution structure of the kallikrein-related peptidases inhibitor SPINK6.

Jung S, Fischer J, Spudy B, Kerkow T, Sönnichsen FD, Xue L, Bonvin AM, Goettig P, Magdolen V, Meyer-Hoffert U, Grötzinger J.

Biochem Biophys Res Commun. 2016 Feb 26;471(1):103-8. doi: 10.1016/j.bbrc.2016.01.172. Epub 2016 Jan 30.

47.

Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students.

Rodrigues JP, Melquiond AS, Bonvin AM.

Biochem Mol Biol Educ. 2016 Mar-Apr;44(2):160-7. doi: 10.1002/bmb.20941. Epub 2016 Jan 11.

48.

Novel Insights into Guide RNA 5'-Nucleoside/Tide Binding by Human Argonaute 2.

Kalia M, Willkomm S, Claussen JC, Restle T, Bonvin AM.

Int J Mol Sci. 2015 Dec 24;17(1). pii: E22. doi: 10.3390/ijms17010022.

49.

Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a.

Deplazes E, Davies J, Bonvin AM, King GF, Mark AE.

J Chem Inf Model. 2016 Jan 25;56(1):127-38. doi: 10.1021/acs.jcim.5b00529. Epub 2015 Dec 24.

PMID:
26642380
50.

Editorial overview: Protein-protein interactions.

Bonvin AM, Keskin Ö.

Curr Opin Struct Biol. 2015 Dec;35:vii-ix. doi: 10.1016/j.sbi.2015.11.004. Epub 2015 Nov 26. No abstract available.

PMID:
26631291

Supplemental Content

Loading ...
Support Center