HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Export

@article{de+vies_07_haddock, abstract = {Here we present version 2.0 of HADDOCK, which incorporates considerable improvements and new features. HADDOCK is now able to model not only protein-protein complexes but also other kinds of biomolecular complexes and multi-component (N > 2) systems. In the absence of any experimental and/or predicted information to drive the docking, HADDOCK now offers two additional ab initio docking modes based on either random patch definition or center-of-mass restraints. The docking protocol has been considerably improved, supporting among other solvated docking, automatic definition of semi-flexible regions, and inclusion of a desolvation energy term in the scoring scheme. The performance of HADDOCK2.0 is evaluated on the targets of rounds 4-11, run in a semi-automated mode using the original information we used in our CAPRI submissions. This enables a direct assessment of the progress made since the previous versions. Although HADDOCK performed very well in CAPRI (65\% and 71\% success rates, overall and for unbound targets only, respectively), a substantial improvement was achieved with HADDOCK2.0.}, author = {de Vries, S. J. and van Dijk, A. D. and Krzeminski, M. and van Dijk, M. and Thureau, A. and Hsu, V. and Wassenaar, T. and Bonvin, A. M.}, citeulike-article-id = {3392931}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/prot.21723}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17803234}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17803234}, comment = {Haddock 2.0 ref. "HADDOCK is now able to model not only protein-protein complexes but also other kinds of biomolecular complexes and multi-component (N > 2) systems."}, day = {1}, doi = {10.1002/prot.21723}, issn = {1097-0134}, journal = {Proteins}, keywords = {algorithm, binding, complexes, docking, download, modelling, ppi, proj\_assembly, structure}, month = {December}, number = {4}, pages = {726--733}, posted-at = {2009-01-14 13:39:14}, priority = {2}, title = {HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets.}, url = {http://dx.doi.org/10.1002/prot.21723}, volume = {69}, year = {2007} }

TY - JOUR ID - de+vies_07_haddock L3 - citeulike-article-id:3392931 N2 - Here we present version 2.0 of HADDOCK, which incorporates considerable improvements and new features. HADDOCK is now able to model not only protein-protein complexes but also other kinds of biomolecular complexes and multi-component (N > 2) systems. In the absence of any experimental and/or predicted information to drive the docking, HADDOCK now offers two additional ab initio docking modes based on either random patch definition or center-of-mass restraints. The docking protocol has been considerably improved, supporting among other solvated docking, automatic definition of semi-flexible regions, and inclusion of a desolvation energy term in the scoring scheme. The performance of HADDOCK2.0 is evaluated on the targets of rounds 4-11, run in a semi-automated mode using the original information we used in our CAPRI submissions. This enables a direct assessment of the progress made since the previous versions. Although HADDOCK performed very well in CAPRI (65% and 71% success rates, overall and for unbound targets only, respectively), a substantial improvement was achieved with HADDOCK2.0. IS - 4 JF - Proteins SN - 1097-0134 EP - 733 TI - HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. VL - 69 SP - 726 KW - algorithm KW - binding KW - complexes KW - docking KW - download KW - modelling KW - ppi KW - proj_assembly KW - structure N1 - Haddock 2.0 ref. "HADDOCK is now able to model not only protein-protein complexes but also other kinds of biomolecular complexes and multi-component (N > 2) systems." AU - de Vries, SJ AU - van Dijk, AD AU - Krzeminski, M AU - van Dijk, M AU - Thureau, A AU - Hsu, V AU - Wassenaar, T AU - Bonvin, AM PY - 2007/12/01/ UR - http://dx.doi.org/10.1002/prot.21723 ER -