Protein-Protein Docking Benchmark - Revision history

Christoph at 04:56, 19 October 2008

2008-10-19T04:56:18Z

Christoph at 05:13, 11 July 2007

2007-07-11T05:13:44Z

Christoph at 23:27, 9 July 2007

2007-07-09T23:27:38Z

Christoph at 23:26, 9 July 2007

2007-07-09T23:26:40Z

Christoph: /* Protein-Protein Docking Benchmark 2.0 */

2007-07-09T22:39:45Z

‎Protein-Protein Docking Benchmark 2.0

Christoph at 07:02, 12 February 2007

2007-02-12T07:02:07Z

Christoph: /* Benchmark table */

2006-09-30T02:31:55Z

‎Benchmark table

Christoph: /* Benchmark table */

2006-09-30T02:29:43Z

‎Benchmark table

Christoph at 02:28, 30 September 2006

2006-09-30T02:28:55Z

Show changes

Christoph: /* Benchmark table */

2006-09-29T23:20:10Z

‎Benchmark table

@@ Line 787: / Line 787: @@
 <div align="center">''Source: Benchmark 2.0<ref name="Mintseris">Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-protein docking benchmark 2.0: an update. ''Proteins, 60(2):214-6''.</ref>''</div>
 </div>
+<br clear="all"/>
 ==Area==
 The area is the mean accessible surface area (ASA) buried by each chain in the pairwise complex:

← Older revision		Revision as of 05:13, 11 July 2007
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	The accessible surface area can also be computed by the NSC program.<ref name="Eisenhaber">Eisenhaber and Argos (1993). ''J Comput Chem, 11:1272-1280''.</ref>		The accessible surface area can also be computed by the NSC program.<ref name="Eisenhaber">Eisenhaber and Argos (1993). ''J Comput Chem, 11:1272-1280''.</ref>
		+
		+	==See also==
		+	*[[Protein-Protein Docking Benchmark 1.0]]

	==References==		==References==

@@ Line 1: / Line 1: @@
-A benchmark of 84 protein-protein interactions with known complexed structures has been developed for testing docking methods<ref name=Mintseris>Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-Protein Docking Benchmark 2.0: an Update. ''Proteins, 60(2):214-6''.</ref>. The set is chosen to cover a wide range of interaction types, and to avoid repeated features, such as the profile of interactors' structural families according to the [http://scop.mrc-lmb.cam.ac.uk/scop/ SCOP] database. Benchmark elements are classified into three levels of difficulty (the most difficult containing the largest change in backbone conformation). The protein-protein docking benchmark contains examples of enzyme-inhibitor, antigen-antibody and homomultimeric complexes.
+A benchmark of 84 protein-protein interactions with known complexed structures has been developed for testing docking methods<ref name="Mintseris">Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-Protein Docking Benchmark 2.0: an Update. ''Proteins, 60(2):214-6''.</ref>. The set is chosen to cover a wide range of interaction types, and to avoid repeated features, such as the profile of interactors' structural families according to the [http://scop.mrc-lmb.cam.ac.uk/scop/ SCOP] database. Benchmark elements are classified into three levels of difficulty (the most difficult containing the largest change in backbone conformation). The protein-protein docking benchmark contains examples of enzyme-inhibitor, antigen-antibody and homomultimeric complexes.
-== Protein-Protein Docking Benchmark 2.0 ==
+See also [http://zlab.bu.edu/julianm/benchmark/ Supplementary Information]
 <div style="float:left; margin:0px 0px 0px 0px;">
 {| align="center" style="border: 1px solid #999; background-color:#FFFFFF"

@@ Line 780: / Line 780: @@
 |colspan="8" style="border-top: 1px solid #333;"|<small>
 '''a''' Complex category labels: E, Enzyme Inhibitor or Enzyme Substrate; A, Antibody Antigen; O, Others; AB, Antigen Bound Antibody.<br/>
-'''b''' RMSD of C&alpha; atoms of interface residues calculated as described previously,<ref>Méndez R, Leplae R, De Maria L, Wodak SJ (2003). Assessment of blind predictions of protein-protein interactions: current status of docking methods. ''Proteins, 52:51-67''.</ref> after finding the best superposition of bound and unbound interfaces.<br/>
+'''b''' RMSD of C&alpha; atoms of interface residues calculated as described previously,<ref name="Mendez">Méndez R, Leplae R, De Maria L, Wodak SJ (2003). Assessment of blind predictions of protein-protein interactions: current status of docking methods. ''Proteins, 52:51-67''.</ref> after finding the best superposition of bound and unbound interfaces.<br/>
-'''c''' Change in accessible surface area upon complex formation calculated using [http://wolf.bms.umist.ac.uk/naccess/ NACCESS].<ref>Hubbard SJ, Thornton JM (1993). NACCESS 2.1.1. ''Deptartment of Biochemistry and Molecular Biology, University College, London''.</ref></small>
+'''c''' Change in accessible surface area upon complex formation calculated using [http://wolf.bms.umist.ac.uk/naccess/ NACCESS].<ref name="Hubbard">Hubbard SJ, Thornton JM (1993). NACCESS 2.1.1. ''Deptartment of Biochemistry and Molecular Biology, University College, London''.</ref></small>
 |}
-<div align="center">''Source: Benchmark 2.0<ref name=Mintseris>Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-protein docking benchmark 2.0: an update. ''Proteins, 60(2):214-6''.</ref>''</div>
+<div align="center">''Source: Benchmark 2.0<ref name="Mintseris">Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-protein docking benchmark 2.0: an update. ''Proteins, 60(2):214-6''.</ref>''</div>
 </div>
 ==References==

@@ Line 16: / Line 16: @@
 !DASA<sup>c</sup> (Å<sup>2</sup>)
 |-
-|-- colspan="8" bgcolor="#eeeeee" | '''Rigid-body (63)'''
+| colspan="8" bgcolor="#eeeeee" | '''Rigid-body (63)'''
 |-
 | 1AVX(A:B)
@@ Line 781: / Line 781: @@
 '''a''' Complex category labels: E, Enzyme Inhibitor or Enzyme Substrate; A, Antibody Antigen; O, Others; AB, Antigen Bound Antibody.<br/>
 '''b''' RMSD of C&alpha; atoms of interface residues calculated as described previously,<ref>Méndez R, Leplae R, De Maria L, Wodak SJ (2003). Assessment of blind predictions of protein-protein interactions: current status of docking methods. ''Proteins, 52:51-67''.</ref> after finding the best superposition of bound and unbound interfaces.<br/>
-'''c''' Change in accessible surface area upon complex formation calculated using NACCESS.<ref>Hubbard SJ, Thornton JM (1993). NACCESS 2.1.1. ''Deptartment of Biochemistry and Molecular Biology, University College, London''.</ref></small>
+'''c''' Change in accessible surface area upon complex formation calculated using [http://wolf.bms.umist.ac.uk/naccess/ NACCESS].<ref>Hubbard SJ, Thornton JM (1993). NACCESS 2.1.1. ''Deptartment of Biochemistry and Molecular Biology, University College, London''.</ref></small>
 |}
 <div align="center">''Source: Benchmark 2.0<ref name=Mintseris>Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-protein docking benchmark 2.0: an update. ''Proteins, 60(2):214-6''.</ref>''</div>

@@ Line 786: / Line 786: @@
 </div>
-== References ==
+==References==
 <references/>
 [[Category:Academic Research]]

@@ Line 1: / Line 1: @@
 A benchmark of 84 protein-protein interactions with known complexed structures has been developed for testing docking methods<ref name=Mintseris>Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-Protein Docking Benchmark 2.0: an Update. ''Proteins, 60(2):214-6''.</ref>. The set is chosen to cover a wide range of interaction types, and to avoid repeated features, such as the profile of interactors' structural families according to the [http://scop.mrc-lmb.cam.ac.uk/scop/ SCOP] database. Benchmark elements are classified into three levels of difficulty (the most difficult containing the largest change in backbone conformation). The protein-protein docking benchmark contains examples of enzyme-inhibitor, antigen-antibody and homomultimeric complexes.
-== Benchmark table ==
+== Protein-Protein Docking Benchmark 2.0 ==
 <div style="float:left; margin:0px 0px 0px 0px;">
 {| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
@@ Line 8: / Line 8: @@
 |--align="center" style="background-color:#1188ee; color:#ffffff;"
 !Complex
-!Cat.
+!Cat.<sup>a</sup>
 !PDBid 1
 !Protein 1

@@ Line 20: / Line 20: @@
 | colspan="8" | Unbound-unbound (16)
 |-
-| 1ACB(E:I) || 5CHA(A) || 1CSE(I) || &alpha;-Chymotrypsin || Eglin C || align="right" | 0.7 || align="right" | 1 || align="right" | 1540
+| {{rcsb|1ACB|1ACB(E:I)}} || 5CHA(A) || 1CSE(I) || &alpha;-Chymotrypsin || Eglin C || align="right" | 0.7 || align="right" | 1 || align="right" | 1540
 |-
 | 1AVW(A:B) || 2PTN || 1BA7(A) || Trypsin || Soybean trypsin inhibitor || align="right" | 0.35 || align="right" | 0 || align="right" | 1740