Protein-Protein Docking Benchmark 2.0: an update.

by: J Mintseris, K Wiehe, B Pierce, R Anderson, R Chen, J Janin, Z Weng

Proteins, Vol. 60, No. 2. (1 August 2005), pp. 214-216.

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Abstract

We present a new version of the Protein-Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound-unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound-unbound cases, with 52 rigid-body cases, 13 medium-difficulty cases, and 7 high-difficulty cases with substantial conformational change. In addition, we retained 12 antibody-antigen test cases with the antibody structure in the bound form. The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2.

@article{benchmark2, abstract = {We present a new version of the Protein-Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound-unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound-unbound cases, with 52 rigid-body cases, 13 medium-difficulty cases, and 7 high-difficulty cases with substantial conformational change. In addition, we retained 12 antibody-antigen test cases with the antibody structure in the bound form. The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2.}, address = {Boston University Bioinformatics Program, Boston, Massachusetts 02215, USA.}, author = {Mintseris, J. and Wiehe, K. and Pierce, B. and Anderson, R. and Chen, R. and Janin, J. and Weng, Z. }, citeulike-article-id = {266165}, doi = {http://dx.doi.org/10.1002/prot.20560}, issn = {1097-0134}, journal = {Proteins}, keywords = {ligand, pka, structure}, month = {August}, number = {2}, pages = {214--216}, posted-at = {2008-07-15 00:32:49}, priority = {5}, title = {Protein-Protein Docking Benchmark 2.0: an update.}, url = {http://dx.doi.org/10.1002/prot.20560}, volume = {60}, year = {2005} }

RIS record

TY - JOUR ID - benchmark2 L3 - citeulike-article-id:266165 TI - Protein-Protein Docking Benchmark 2.0: an update. JF - Proteins VL - 60 IS - 2 SP - 214 EP - 216 AD - Boston University Bioinformatics Program, Boston, Massachusetts 02215, USA. SN - 1097-0134 N2 - We present a new version of the Protein-Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound-unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound-unbound cases, with 52 rigid-body cases, 13 medium-difficulty cases, and 7 high-difficulty cases with substantial conformational change. In addition, we retained 12 antibody-antigen test cases with the antibody structure in the bound form. The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2. KW - ligand KW - pka KW - structure AU - Mintseris, J AU - Wiehe, K AU - Pierce, B AU - Anderson, R AU - Chen, R AU - Janin, J AU - Weng, Z PY - 2005/08/01/ UR - http://dx.doi.org/10.1002/prot.20560 ER -

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