Approximate Ensembles
Approximate Path Ensembles
Statistical Rotamer Libraries
Boltzmann Ensembles

Sets of physically and chemically reasonable structures generated using a fairly crude method, but with substantial structural diversity.  (More details). Ensemble files include computational details.

Protein Related PDB codes Number of Residues Description Ensemble File
(PDB format)
Number of structures
Human CDC25B Catalytic Domain 1QB0 177 all-atom 1qb0.aa.pdb.gz 495
coarse-grained n/a n/a
D-Galactose/D-Glucose Binding Protein 2GBP 309 all-atom 2gbp.aa.pdb.gz 297
coarse-grained n/a n/a
Calmodulin 1CFD 72 all-atom 1cfd.aa.pdb.gz 196
coarse-grained 1cfd.cg.pdb.gz 200
Barstar 1A19 89 all-atom 1a19.aa.pdb.gz  191
coarse-grained 1a19.cg.pdb.gz 200
Ferredoxin II 1FXD 58 all-atom 1fxd.aa.pdb.gz 141
coarse-grained 1fxd.cg.pdb.gz 200
Alpha-Amylase inhibitor 1HOE 74 all-atom 1hoe.aa.pdb.gz 129
coarse-grained 1hoe.cg.pdb.gz 200

Approximate path ensembles consist of all-atom configurations connecting the two indicated PDB structures. Paths were generated based on coarse-grained simulation followed by addition of atomistic detail.  (More details)

Protein Starting PDB Ending PDB Number of Residues Description Ensemble File
(PDB format)
Number of Paths
Lymphotactin 2HDM 2JP1 75 all-atom 2hdm-to-2jp1.tgz 20
Calmodulin 1CFD 1CLL 72 all-atom 1cfd-to-1cll.tgz 38

All-atom side-chain configurations distributed according to the indicated forcefield and solvent model. (More details)

Side-chain

Forcefield

Solvent Model

Rotamer-classified?

Ensemble File
(PDB format)

Number of configurations

Met

OPLS-AA

GB/SA

No

metsc.tgz
29MB

80,000

Phe

OPLS-AA

GB/SA

No

phesc.tgz
18MB

40,000

Tyr

OPLS-AA

GB/SA

No

tyrsc.tgz
53MB

110,000


Molecular fragment libraries distributed according to the indicated forcefield and solvent model. (More details)

Fragment

Forcefield

Solvent Model

Ensemble File
(PDB format)

Number of configurations

Ace

OPLS-AA

Uniform dielectric with ε=60

ace.tgz

10,000

Ace-Ala

OPLS-AA

Uniform dielectric with ε=60

ace-ala.tgz

10,000

Ala

OPLS-AA

Uniform dielectric with ε=60

ala.tgz

10,000

Nme

OPLS-AA

Uniform dielectric with ε=60

nme.tgz

10,000

Structures distributed according to Boltzmann-factor weighting using a specified forcefield and solvent model.  (More details)

Protein

Description

Related PDB codes

Ensemble
(PDB format)

Forcefield/
Solvent model

Number of structures

None available yet