This page enumerates benchmark systems for assessing the accuracy of protein force fields and tracks which individuals or groups are responsible for running each benchmark simulation. Benchmark systems are organized into tiers with increasing complexity for each tier.

In the tables below, short name is the string used to identify the benchmark target in the proteinbenchmark repo here:

. Type is one of peptide, folded, or disordered and is used to determine the default solvent padding and simulation length. For the folded type, the CATH domain classification (https://www.cathdb.info/wiki) is provided in parentheses. Starting model is either extended or a PDB ID. N residues is the number of protein residues. N solvated atoms is the total number of atoms (protein+water+ions) in the solvated system.

Tier 1 (rapid evaluation)

Target name	Short name	Type	Starting model	N residues	N solvated atoms	Simulator

Target name	Short name	Type	Starting model	N residues	N solvated atoms	Simulator
Trialanine	ala3	Peptide	Extended	3	1409	@Chapin Cavender
Tetraalanine	ala4	Peptide	Extended	4	1824	@Chapin Cavender
Pentaalanine	ala5	Peptide	Extended	5	2614	@Chapin Cavender
Hexaalanine	ala6	Peptide	Extended	6	3680	@Chapin Cavender
Heptaalanine	ala7	Peptide	Extended	7	4848	@Chapin Cavender
Triglycine	gly3	Peptide	Extended	3	1430	@Chapin Cavender
Trivaline	val3	Peptide	Extended	3	1400	@Chapin Cavender
Gly-Ala-Gly	gag	Peptide	Extended	3	1427	@Chapin Cavender
Gly-Glu-Gly	geg	Peptide	Extended	3	1409	@Chapin Cavender
Gly-Phe-Gly	gfg	Peptide	Extended	3	1395	@Chapin Cavender
Gly-Lys-Gly	gkg	Peptide	Extended	3	1401	@Chapin Cavender
Gly-Leu-Gly	glg	Peptide	Extended	3	1409	@Chapin Cavender
Gly-Met-Gly	gmg	Peptide	Extended	3	1407	@Chapin Cavender
Gly-Ser-Gly	gsg	Peptide	Extended	3	1425	@Chapin Cavender
Gly-Val-Gly	gvg	Peptide	Extended	3	1409	@Chapin Cavender

Tier 2 (select release candidate)

Target name	Short name	Type	Starting model	N residues	N solvated atoms	Simulator

Target name	Short name	Type	Starting model	N residues	N solvated atoms	Simulator
Ace-(AAQAA)3-NH2	aaqaa3	Disordered	Extended	16	26733	@Chapin Cavender
Bovine pancreatic trypsin inhibitor	bpti	Folded (4.10.410.10)	PDB 1PIT	58	10899	@Chapin Cavender
Streptococcal protein G third immonuglobulin-binding domain	gb3	Folded (3.10.23.10)	PDB 1P7E	56	7668	@Chapin Cavender
Hen egg white lysozyme	hewl	Folded (1.10.530.10)	PDB 1E8L	129	16787	@Chapin Cavender
Human ubiquitin	ubq	Folded (3.10.20.90)	PDB 1D3Z	76	14741	@Chapin Cavender

Tier 3 (assess release candidate)

Target name	Short name	Type	Starting model	N residues	N solvated atoms	Simulator

Target name	Short name	Type	Starting model	N residues	N solvated atoms	Simulator
Amyloid β (1-40)	ab40	Disordered	Extended	40	291473
Alpha-synuclein	asyn	Disordered	Extended	140	7333819
NESG target CcR55	ccr55	Folded (3.20.170.20)	PDB 2JQN	116	14194	@Lily Wang
NESG target CtR148A	ctr148a	Folded (3.30.70.260)	PDB 2KO1	88	27180	@Lily Wang
NESG target DhR29B	dhr29b	Folded (2.170.120.30)	PDB 2KPU	96	45762	@Lily Wang
NESG target DhR8C	dhr8c	Folded (2.60.40.2000)	PDB 2KYI	161	17793	@Julianne Hoeflich
NESG target ER382A	er382a	Folded (2.30.30.100)	PDB 2JN0	53	7149	@Julianne Hoeflich
NESG target MrR110B	mrr110b	Folded (2.40.50.140)	PDB 2K5V	269	20815	@Lily Wang
NESG target PsR293	psr293	Folded (3.90.1150.30)	PDB 2KFP	125	33612	@Lily Wang
NESG target SR478	sr478	Folded (6.10.140.40)	PDB 2JS1	80	45881	@Lily Wang
NESG target SrR115C	srr115c	Folded (1.25.40.10)	PDB 2KCV	99	14547	@Julianne Hoeflich
NESG target StR65	str65	Folded (1.20.1290.30)	PDB 2JN8	110	21860	@Lily Wang
NESG target XcR50	xcr50	Folded (3.40.30.10)	PDB 1XPV	78	10709	@Julianne Hoeflich

Small molecule physical properties

This section describes physical property calculations run using OpenFF Evaluator or OpenFE Pontibus rather than the proteinbenchmark repo.

Target name	Type	Ligand FF	Water model	Simulator

Target name	Type	Ligand FF	Water model
Mixture densities/enthalpies	Small molecule	OpenFF 3.0.0 alpha0	TIP3P
Mixture densities/enthalpies	Small molecule	OpenFF 3.0.0 alpha0	OPC3
MNSol	Small molecule	OpenFF 3.0.0 alpha0	TIP3P
MNSol	Small molecule	OpenFF 3.0.0 alpha0	OPC3
FreeSolv	Small molecule	OpenFF 3.0.0 alpha0	TIP3P
FreeSolv	Small molecule	OpenFF 3.0.0 alpha0	OPC3

Protein-ligand benchmarks

This section describes relative binding free energy calculations run using OpenFE Pontibus rather than the proteinbenchmark repo.

Target name	Type	Protein FF	Ligand FF	Water model	Simulator	Alchemiscale scope

Target name	Type	Protein FF	Ligand FF	Water model	Simulator	Alchemiscale scope
JACS dataset	RBFE	ff14SB OFFXML	OpenFF 2.2.1	TIP3P	@Irfan Alibay	omsf-pontibus_0_2_0-openff_2_2_1_ff14sb_tip3p_*

Protein benchmark systems

Tier 1 (rapid evaluation)

Tier 2 (select release candidate)

Tier 3 (assess release candidate)

Small molecule physical properties

Protein-ligand benchmarks