Skip to main content

Table 4 Comparison of flexible loops detected by MSU-FIRST, KINARI v1.0, and RigidFinder on four proteins.

From: Towards accurate modeling of noncovalent interactions for protein rigidity analysis

Protein

PDB

MSU-FIRST

KINARI v1.0

RigidFinder

LAO-binding 1

LAO-binding 2

1lst

2lao

1

1

1

1

1

1

HIV-1 Protease 1

HIV-1 Protease 2

1hhp

1htg

3

4

3

3

2

2

Dihydrofolate Reductase 1

Dihydrofolate Reductase 2

Dihydrofolate Reductase 3

1ra1

1rx1

1rx6

2

2

2

2

1

2

2

2

2

Adenylate Kinase 1

Adenylate Kinase 2

1aky

1dvr

6

4

6

4

3

3

  1. A comparison of the flexible loop regions detected by KINARI v1.0, MSU-FIRST, and RigidFinder. The four proteins, with annotated flexible loops, were used in the validation of MSU-FIRST [1, 5]. The table data for MSU-FIRST was taken from the same publications. For KINARI v1.0 and RigidFinder, flexible loops were determined visually. Because RigidFinder computes decompositions based on multiple conformations, the results shown will match for all conformations of the same protein.
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us