Covalent docking using autodock: two-point attractor and flexible side chain methods.
Open accessAbstract
We describe two methods of automated covalent docking using Autodock4: the two‐point attractor method and the flexible side chain method. Both methods were applied to a training set of 20 diverse protein–ligand covalent complexes, evaluating their reliability in predicting the crystallographic pose of the ligands. The flexible side chain method performed best, recovering the pose in 75% of cases, with failures for the largest inhibitors tested. Both methods are freely available at the AutoDock website (http://autodock.scripps.edu).
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TL;DR
Two covalent docking protocols for AutoDock4 were compared on 20 diverse protein–ligand covalent complexes: a two-point attractor method and a flexible side chain method. The flexible side chain method reproduced crystallographic poses in 75% of cases, versus 20% for the two-point attractor method.
Key findings
- The flexible side chain method recovered the experimental pose in 15/20 systems (75% success), while the two-point attractor method succeeded in 4/20 systems (20%).
- For the two-point attractor method, RMSD between docked and experimental Cα/Cβ atoms was always <0.09 Å, so it formed the covalent bond effectively, but it was more prone to false-positive poses with RMSD values as high as 6 Å.
- Accuracy correlated with ligand torsional complexity: the two-point attractor method had only one success with ligands over 9 torsional degrees of freedom, whereas the flexible side chain method succeeded with up to 14 torsions.
- Both methods failed on complex 3lok (7 torsions), attributed to the absence of a coordinating water between ligand and Glu339, and neither redocked 1w3c because a large ligand fraction was solvent-exposed.
Methods
- AutoDock4 was modified in two ways: the two-point attractor method uses modified interaction maps and special atom types X/Z with a Gaussian Z-potential centered at the covalent attachment site; the flexible side chain method tethers the ligand to the target residue and treats the ligand–residue as a fully flexible side chain with a rigid protein backbone.
- The dataset comprised 20 PDB covalent complexes from 19 protein families, with X-ray resolution ≤2.65 Å, Ser or Cys covalent residues, no binding-site cofactors, ligand torsional degrees of freedom from 6 to 20, and molecular weights from 369 to 738 Da.
- Docking used the Lamarckian Genetic Algorithm; success was defined as lowest-energy pose RMSD <3.0 Å from experimental coordinates, and results were clustered with 2.0 Å RMSD tolerance.
Limitations
- Stated: the flexible side chain method failed for the largest inhibitors tested; both methods failed on 3lok due to missing coordinating water and on 1w3c due to solvent-exposed ligand rings; the two-point attractor method allows approximation in covalent attachment position, which may help with apo structures but was still being assessed.
- Evident: the benchmark is small (20 complexes, 19 families) and limited to Ser/Cys covalent residues, so generalization to other covalent residues or larger libraries is not established.
- Evident: the flexible side chain method assumes a rigid protein backbone, and the study reports pose-prediction accuracy rather than prospective virtual-screening performance.
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- Findingown data
No significant variations were found in the overall success rate of the two-point attractor method between default and extended LGA settings.
“Energies improved slightly when going from default LGA settings (Table 3 in Supporting Information) to extended settings (Table 4 in Supporting Information), but no significant variations were found in the overall success rate.”
Quote in the paperNot a substantial claim - Findingown data
The flexible side chain method recovered the crystallographic pose in 75% of cases (15 out of 20 systems) in the training set.
“The flexible side chain method performed best, recovering the pose in 75% of cases, with failures for the largest inhibitors tested.”
- Also stated in: § Results and Discussion · plain
“Accuracy of the flexible side chain method is considerably higher, reproducing experimental coordinates in 15 out of 20 systems (75% success rate).”
Quote in the paperSubstantial claim - Also stated in: § Results and Discussion · plain
- Findingreasoning
Search efficiency is more effective with the flexible residue method than with the two-point attractor method.
“As expected, search efficiency is more effective with the flexible residue method than with the two-point attractor method.”
Quote in the paperSubstantial claim - Findingown data
The success rate of both methods showed a correlation with the complexity of the ligands, decreasing accuracy with the increase of torsional degrees of freedom.
“The success rate of both methods showed a correlation with the complexity of the ligands, decreasing accuracy with the increase of torsional degrees of freedom.”
Quote in the paperNot a substantial claim - Findingreasoning
The flexible side chain method obtained successful results with up to 14 torsional degrees of freedom.
“As expected, because of the reduction in degrees of freedom in the tethered docking method, it is less sensitive than the two-point attractor method to the torsional complexity of the ligands, obtaining successful results with up to 14 torsional degrees of freedom [Fig.3(b)].”
Quote in the paperSubstantial claim
- Findingown data
The flexible side chain method provided better accuracy than the two-point attractor method.
“The flexible side chain method performed best, recovering the pose in 75% of cases, with failures for the largest inhibitors tested.”
Quote in the paperSubstantial claim - Findingown data
Only one successful result was obtained with ligands over 9 torsional degrees of freedom for the two-point attractor method.
“Also, accuracy is roughly correlated with the number of rotatable bonds of the ligand [Fig.3(a)], with only one successful result with ligands over 9 torsional degrees of freedom.”
Quote in the paperSubstantial claim - Findingreasoning
The flexible side chain method is less sensitive than the two-point attractor method to the torsional complexity of the ligands.
“As expected, because of the reduction in degrees of freedom in the tethered docking method, it is less sensitive than the two-point attractor method to the torsional complexity of the ligands, obtaining successful results with up to 14 torsional degrees of freedom [Fig.3(b)].”
Quote in the paperSubstantial claim - Findingown data
For the two-point attractor method, the RMSD between the Ca and Cb of the docked poses and the experimental coordinates were all less than 0.09 Å.
“For the two-point attractor method, the RMSD between the Ca and Cb of the docked poses and the experimental coordinates were all less than 0.09 A ˚, so the method is effective for forming the covalent bond.”
Quote in the paperSubstantial claim - Findingown data
Accuracy of the two-point attractor method is roughly correlated with the number of rotatable bonds of the ligand.
“Also, accuracy is roughly correlated with the number of rotatable bonds of the ligand [Fig.3(a)], with only one successful result with ligands over 9 torsional degrees of freedom.”
Quote in the paperSubstantial claim - Findingreasoning
Highly flexible ligands showed poorer reliability in finding the correct result, as observed in the larger number of scarcely populated clusters for very flexible ligands.
“Overall, highly flexible ligands showed poorer reliability in finding the correct result, as observed in the larger number of scarcely populated clusters for very flexible ligands.”
Quote in the paperSubstantial claim - Findingown data
The two-point attractor method reproduced the experimental coordinates in 4 out of 20 systems (20% success rate).
“Overall, the two-point attractor method performed poorly, reproducing the experimental coordinates in 4 systems out of 20 (20% success rate).”
Quote in the paperSubstantial claim - Findingreasoning
The optimal values selected for the Gaussian Z-potential were d = 3 Å and e = 10 kcal/mol.
“The optimal values selected were d 5 3 A ˚, and e 5 10 kcal/mol.”
Quote in the paperNot a substantial claim - Findingreasoning
Both methods fail with complex 3lok (7 torsions).
“Both methods are successful with low torsional degrees of freedom (6, 7, and 8 for 2awz, 18 3c9w, 19 and 1pwc, 17 respectively), but they both fail with complex 3lok 20 (7 torsions).”
Quote in the paperSubstantial claim - Findingreasoning
Neither method is successful in redocking the complex 1w3c.
“Also, neither method is successful in redocking the complex 1w3c, 21 due to the large fraction of the ligand (i.e., thiophene and indole rings) exposed to the solvent.”
Quote in the paperSubstantial claim - Findingreasoning
Extreme value pairs (high-d/low-e, low-d/high-e) resulted in the worst results with higher deviations from the experimental poses.
“As expected, extreme value pairs (i.e., high-d/low-e, lowd/high-e) resulted in the worst results with higher deviations from the experimental poses.”
Quote in the paperSubstantial claim - Interpretationreasoning
The two-point attractor method is more prone to finding false-positive poses that can be ranked higher than the correct pose, resulting in RMSD values as high as 6 Å.
“Therefore, the two-point attractor method is more prone to finding false-positive poses that can be ranked higher than the correct pose, resulting in RMSD values as high as 6 A ˚.”
Quote in the paperSubstantial claim - Interpretationown data
The failure to redock 1w3c is due to the large fraction of the ligand (thiophene and indole rings) exposed to the solvent.
“Also, neither method is successful in redocking the complex 1w3c, 21 due to the large fraction of the ligand (i.e., thiophene and indole rings) exposed to the solvent.”
Quote in the paperSubstantial claim - Interpretationown data
The two-point attractor method is effective for forming the covalent bond.
“For the two-point attractor method, the RMSD between the Ca and Cb of the docked poses and the experimental coordinates were all less than 0.09 A ˚, so the method is effective for forming the covalent bond.”
Quote in the paperSubstantial claim - Interpretationown data
The failure with complex 3lok is due to the absence of co-ordinating water between the ligand and residue Glu339.
“This is due to the absence of co-ordinating water between the ligand and residue Glu339 (data not shown).”
Quote in the paperSubstantial claim - Interpretationown data
The flexible residue method provides the most effective approach in simulating covalent ligands, based on the results from the data set.
“Based on the results from the data set, the flexible residue method provides the most effective approach in simulating covalent ligands.”
Quote in the paperSubstantial claim - Interpretationreasoning
The two-point attractor method's untethered docking results in larger numbers of degrees of freedom, making the search implicitly more complex.
“Since the ligand is docked untethered with the two-point attractor method, it results in larger numbers of degrees of freedom, making the search implicitly more complex.”
Quote in the paperSubstantial claim - Interpretationnone given
With both methods, it is possible to model the most frequently covalently modified residues, such as cysteine, lysine, threonine, and serine.
“With both methods, it is possible to model the most frequently covalently modified residues, such as cysteine, lysine, threonine, and serine.”
Quote in the paperNot a substantial claim
- May combine two claims. 5
- Classified as probably not a substantial claim. 5
- The quote only partly states this claim. 1
May combine two claims.
Findingown dataMost tested values of Gaussian potential coefficients d and e provided satisfying results, with several combinations achieving RMSD below 1.0 Å.
“Most values provided satisfying results, with several combinations achieving RMSD below 1.0 A ˚.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataEnergies improved slightly when going from default LGA settings to extended settings for the two-point attractor method.
“Energies improved slightly when going from default LGA settings (Table 3 in Supporting Information) to extended settings (Table 4 in Supporting Information), but no significant variations were found in the overall success rate.”
Quote in the paperNot a substantial claimThe quote only partly states this claim.
Findingnone givenBoth methods are successful with low torsional degrees of freedom (6, 7, and 8 for 2awz, 3c9w, and 1pwc respectively).
“Both methods are successful with low torsional degrees of freedom (6, 7, and 8 for 2awz, 18 3c9w, 19 and 1pwc, 17 respectively), but they both fail with complex 3lok 20 (7 torsions).”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Interpretationnone givenBoth methods provide examples of how AutoDock suite parameters can be customized to implement new methods and extend basic functionalities.
“Finally, both methods provide examples of how Auto-Dock suite parameters can be customized to implement new methods and extend basic functionalities.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningConversely, large d and small e will be easier to reach during the search, but it will provide lower precision in reproducing the covalent geometry.
“Conversely, large d and small e will be easier to reach during the search, but it will provide lower precision in reproducing the covalent geometry.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S4 (based).
Interpretationnone givenThe two-point attractor method allows incorporation of a certain degree of approximation in the position of the covalent attachment, which may be important for accommodating conformational changes in residue backbone structure surrounding the site of the covalent ligand (e.g., when docking in apo structures).
“The two-point attractor method, on the other hand, allows incorporation of a certain degree of approximation in the position of the covalent attachment, which may be important for accommodating any conformational changes in residue backbone structure surrounding the site of the covalent ligand (i.e., when docking in apo structures).”
Quote in the paperNot a substantial claimMay combine two claims.
PremisecitationThe specification and architecture of AutoDock was designed to allow user modification for specialized systems, and has been used previously to model protein flexibility, flexible rings in ligands, zinc interaction, and selective hydration.
“The specification and architecture of AutoDock was designed to allow this type of user modification for specialized systems, and has been used previously to model protein flexibility, 12 flexible rings in ligands, 13 zinc interaction, 14 and selective hydration.15”
Quote in the paperSubstantial claim0 of 3 sources checkedMay combine two claims.
InterpretationreasoningIn the flexible side chain method, the ligand is properly aligned along the Ca-Cb bond and only torsional degrees of freedom need to be searched, whereas the two-point attractor method needs to expend much computational effort finding and optimizing the location and orientation of the covalent bond at the site of attachment.
“In the flexible side chain method, the ligand is properly aligned along the Ca-Cb bond and only torsional degrees of freedom need to be searched, whereas the two-point attractor method needs to expend much computational effort finding and optimizing the location and orientation of the covalent bond at the site of attachment.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductcitationThe two-point attractor method's ligand PDBQT coordinates were randomized (orientation, translation, and torsions) using AutoDock Vina to prevent bias toward the known input ligand configuration.
“Hydrogens and charges were added, and to prevent any bias toward the known input ligand configuration, the resulting PDBQT coordinates were randomized (orientation, translation, and torsions) using AutoDock Vina.16”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [16]
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationPreviously reported results suggest that the AutoDock flexible residue method outperformed GOLD in a dataset of 76 complexes.
“Previously reported results suggest that AutoDock flexible residue method outperformed GOLD in a dataset of 76 complexes.4”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [4] source
Not checked in the free run.
May combine two claims.
InterpretationreasoningThe combination of small d and large e results in a narrow and deep potential, whose energetic minimum will be accurately located on the atom position, but will be much harder to find during the search.
“The combination of small d and large e results in a narrow and deep potential, whose energetic minimum will be accurately located on the atom position, but will be much harder to find during the search.”
Quote in the paperSubstantial claim
The authors state this as an assumption.
The protein backbone is rigid in the flexible side chain method.
“In our approach, which assumes a rigid protein backbone, Ca and Cb atoms are fixed in space while all torsions of both ligand and residue (including Ca-Cb) are allowed to rotate [Fig.1(b)].”
Claims other papers make about this one
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GOLD, Autodock4, CovalentDock, CovDock, DOCKovalent, and DOCK-TITE are examples of docking programs that developed specific methodologies to deal with covalent docking.
“GOLD (Jones et al., 1997), Autodock4 (Bianco et al., 2016), CovalentDock (Ouyang et al., 2013), CovDock (Zhu et al., 2014), DOCKovalent (London et al., 2014), and DOCK-TITE (Scholz et al., 2015) are some examples of docking programs that developed specific methodologies to deal with covalent-docking.”
From Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges (2018) · cites this paper as Bianco et al., 2016
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- Authors
- Bianco, G., Forli, S., Goodsell, D. S., & Olson, A. J.
- Affiliations
- University of Cagliari (IT)
- Scripps Research Institute (US)
- Corresponding author
- Olson, Arthur J.
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2015-07-07
- Volume
- 25
- Issue
- 1
- Pages
- 295-301
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- PMC
- PMC4815316
- OpenAlex
- W1931365650
- Semantic Scholar
- 8162cd069657b91b50cf5d9398dd13a75b294833
- Cited by
- 246
- References
- 21
- Citations by year
- 2026: 25 · 2025: 30 · 2024: 30 · 2023: 29 · 2022: 24 · 2021: 29 · 2020: 26 · 2019: 24 · 2018: 13 · 2017: 10 · 2016: 5 · 2015: 1
- FWCI
- 10.28
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Protein Science (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (R01 GM069832)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- covalent docking, protein-ligand complex, ligand pose prediction, covalent inhibitors
- MeSH terms
- Automation, Ligands, Proteins, Molecular Docking Simulation
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