Search Results - "Bonvin, A M"

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 by Kurkcuoglu, Zeynep, Koukos, Panagiotis I., Citro, Nevia, Trellet, Mikael E., Rodrigues, J. P. G. L. M., Moreira, Irina S., Roel-Touris, Jorge, Melquiond, Adrien S. J., Geng, Cunliang, Schaarschmidt, Jörg, Xue, Li C., Vangone, Anna, Bonvin, A. M. J. J.

“…We present the performance of HADDOCK, our information-driven docking software, in the second edition of the D3R Grand Challenge. In this blind experiment,…”
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Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 by Vangone, A., Rodrigues, J. P. G. L. M., Xue, L. C., van Zundert, G. C. P., Geng, C., Kurkcuoglu, Z., Nellen, M., Narasimhan, S., Karaca, E., van Dijk, M., Melquiond, A. S. J., Visscher, K. M., Trellet, M., Kastritis, P. L., Bonvin, A. M. J. J.

“…ABSTRACT Our information‐driven docking approach HADDOCK is a consistent top predictor and scorer since the start of its participation in the CAPRI…”
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Integrative Modelling of Biomolecular Complexes by Koukos, P.I., Bonvin, A.M.J.J.

“…In recent years, the use of integrative, information-driven computational approaches for modeling the structure of biomolecules has been increasing in…”
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The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes by van Zundert, G.C.P., Rodrigues, J.P.G.L.M., Trellet, M., Schmitz, C., Kastritis, P.L., Karaca, E., Melquiond, A.S.J., van Dijk, M., de Vries, S.J., Bonvin, A.M.J.J.

“…The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and…”
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The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes by van Zundert, G.C.P., Trellet, M., Schaarschmidt, J., Kurkcuoglu, Z., David, M., Verlato, M., Rosato, A., Bonvin, A.M.J.J.

“…Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software…”
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DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes by van Zundert, G C P, Bonvin, A M J J

“…We present DisVis, a Python package and command line tool to calculate the reduced accessible interaction space of distance-restrained binary protein…”
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Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli by Singh, S, Folkers, G. E., Bonvin, A. M. J. J., Boelens, R, Wechselberger, R, Niztayev, A, Kaptein, R

“…The C‐terminal domain of the UvrC protein (UvrC CTD) is essential for 5′ incision in the prokaryotic nucleotide excision repair process. We have determined the…”
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Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids by van Zundert, G.C.P., Bonvin, A.M.J.J.

“…Cryo-electron microscopy provides fascinating structural insight into large macromolecular machines at increasing detail. Despite significant advances in the…”
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Sense and Simplicity in HADDOCK Scoring: Lessons from CASP‐CAPRI (page 418) by Vangone, A., Rodrigues, J. P. G. L. M., Xue, L. C., van Zundert, G. C. P., Geng, C., Kurkcuoglu, Z., Nellen, M., Narasimhan, S., Karaca, E., van Dijk, M., Melquiond, A. S. J., Visscher, K. M., Trellet, M., Kastritis, P. L., Bonvin, A. M. J. J.

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Two-rung Model of a Left-handed β-Helix for Prions Explains Species Barrier and Strain Variation in Transmissible Spongiform Encephalopathies by Langedijk, J.P.M., Fuentes, G., Boshuizen, R., Bonvin, A.M.J.J.

“…In this study, a new β-helical model is proposed that explains the species barrier and strain variation in transmissible spongiform encephalopathies. The…”
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Data-driven docking: HADDOCK's adventures in CAPRI by van Dijk, A. D. J., de Vries, S. J., Dominguez, C., Chen, H., Zhou, H.-X., Bonvin, A. M. J. J.

“…We have shown previously that given high‐resolution structures of the unbound molecules, structure determination of protein complexes is possible by including…”
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IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods by Vallat, Brinda, Webb, Benjamin M., Westbrook, John D., Goddard, Thomas D., Hanke, Christian A., Graziadei, Andrea, Peisach, Ezra, Zalevsky, Arthur, Sagendorf, Jared, Tangmunarunkit, Hongsuda, Voinea, Serban, Sekharan, Monica, Yu, Jian, Bonvin, Alexander A.M.J.J., DiMaio, Frank, Hummer, Gerhard, Meiler, Jens, Tajkhorshid, Emad, Ferrin, Thomas E., Lawson, Catherine L., Leitner, Alexander, Rappsilber, Juri, Seidel, Claus A.M., Jeffries, Cy M., Burley, Stephen K., Hoch, Jeffrey C., Kurisu, Genji, Morris, Kyle, Patwardhan, Ardan, Velankar, Sameer, Schwede, Torsten, Trewhella, Jill, Kesselman, Carl, Berman, Helen M., Sali, Andrej

“…[Display omitted] •Data standard for macromolecular structures from integrative and hybrid modeling (IHM).•Infrastructure for deposition, archiving, and public…”
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1H, 13C and 15N assignment of the GNA1946 outer membrane lipoprotein from Neisseria meningitidis by Neumoin, A., Leonchiks, A., Petit, P., Vuillard, L., Pizza, M., Soriani, M., Boelens, R., Bonvin, A. M. J. J.

“…GNA1946 (Genome-derived Neisseria Antigen 1946) is a highly conserved exposed outer membrane lipoprotein from Neisseria meningitidis bacteria of 287 amino acid…”
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3D-DART: a DNA structure modelling server by van Dijk, Marc, Bonvin, Alexandre M. J. J.

“…There is a growing interest in structural studies of DNA by both experimental and computational approaches. Often, 3D-structural models of DNA are required,…”
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Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations by Bonvin, A M, Vis, H, Breg, J N, Burgering, M J, Boelens, R, Kaptein, R

“…The Arc repressor of Salmonella bacteriophage P22 is a dimeric sequence-specific DNA-binding protein. The solution structure of Arc has been determined from 2D…”
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"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin by Bonvin, A M, Rullmann, J A, Lamerichs, R M, Boelens, R, Kaptein, R

“…The structure in solution of crambin, a small protein of 46 residues, has been determined from 2D NMR data using an iterative relaxation matrix approach (IRMA)…”
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INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures by Salomoni, D., Campos, I., Gaido, L., de Lucas, J. Marco, Solagna, P., Gomes, J., Matyska, L., Fuhrman, P., Hardt, M., Donvito, G., Dutka, L., Plociennik, M., Barbera, R., Blanquer, I., Ceccanti, A., Cetinic, E., David, M., Duma, C., López-García, A., Moltó, G., Orviz, P., Sustr, Z., Viljoen, M., Aguilar, F., Alves, L., Antonacci, M., Antonelli, L. A., Bagnasco, S., Bonvin, A. M. J. J., Bruno, R., Chen, Y., Costa, A., Davidovic, D., Ertl, B., Fargetta, M., Fiore, S., Gallozzi, S., Kurkcuoglu, Z., Lloret, L., Martins, J., Nuzzo, A., Nassisi, P., Palazzo, C., Pina, J., Sciacca, E., Spiga, D., Tangaro, M., Urbaniak, M., Vallero, S., Wegh, B., Zaccolo, V., Zambelli, F., Zok, T.

“…This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud…”
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Direct NOE refinement of biomolecular structures using 2D NMR data by Bonvin, A M, Boelens, R, Kaptein, R

“…A set of computer programs called DINOSAUR has been developed, which allows the refinement of biomolecular structures directly from 2D NOE intensities. The NOE…”
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protein-DNA docking benchmark by van Dijk, Marc, Bonvin, Alexandre M.J.J

“…We present a protein-DNA docking benchmark containing 47 unbound-unbound test cases of which 13 are classified as easy, 22 as intermediate and 12 as difficult…”
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The solution structure of the human retinoic acid receptor-beta DNA-binding domain by Knegtel, R M, Katahira, M, Schilthuis, J G, Bonvin, A M, Boelens, R, Eib, D, van der Saag, P T, Kaptein, R

“…The three-dimensional structure of the DNA-binding domain of the human retinoic acid receptor-beta (hRAR-beta) has been determined by nuclear magnetic…”
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