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Simpkin AJ, Rodríguez FS, Mesdaghi S, Kryshtafovych A, Rigden DJ. Evaluation of model refinement in CASP14. Proteins 2021; 89:1852-1869. [PMID: 34288138 PMCID: PMC8616799 DOI: 10.1002/prot.26185] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/19/2021] [Accepted: 07/11/2021] [Indexed: 12/15/2022]
Abstract
We report here an assessment of the model refinement category of the 14th round of Critical Assessment of Structure Prediction (CASP14). As before, predictors submitted up to five ranked refinements, along with associated residue-level error estimates, for targets that had a wide range of starting quality. The ability of groups to accurately rank their submissions and to predict coordinate error varied widely. Overall, only four groups out-performed a "naïve predictor" corresponding to the resubmission of the starting model. Among the top groups, there are interesting differences of approach and in the spread of improvements seen: some methods are more conservative, others more adventurous. Some targets were "double-barreled" for which predictors were offered a high-quality AlphaFold 2 (AF2)-derived prediction alongside another of lower quality. The AF2-derived models were largely unimprovable, many of their apparent errors being found to reside at domain and, especially, crystal lattice contacts. Refinement is shown to have a mixed impact overall on structure-based function annotation methods to predict nucleic acid binding, spot catalytic sites, and dock protein structures.
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Affiliation(s)
- Adam J. Simpkin
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Filomeno Sánchez Rodríguez
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Shahram Mesdaghi
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | | | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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2
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Røgen P. Quantifying steric hindrance and topological obstruction to protein structure superposition. Algorithms Mol Biol 2021; 16:1. [PMID: 33639968 PMCID: PMC7913338 DOI: 10.1186/s13015-020-00180-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 12/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In computational structural biology, structure comparison is fundamental for our understanding of proteins. Structure comparison is, e.g., algorithmically the starting point for computational studies of structural evolution and it guides our efforts to predict protein structures from their amino acid sequences. Most methods for structural alignment of protein structures optimize the distances between aligned and superimposed residue pairs, i.e., the distances traveled by the aligned and superimposed residues during linear interpolation. Considering such a linear interpolation, these methods do not differentiate if there is room for the interpolation, if it causes steric clashes, or more severely, if it changes the topology of the compared protein backbone curves. RESULTS To distinguish such cases, we analyze the linear interpolation between two aligned and superimposed backbones. We quantify the amount of steric clashes and find all self-intersections in a linear backbone interpolation. To determine if the self-intersections alter the protein's backbone curve significantly or not, we present a path-finding algorithm that checks if there exists a self-avoiding path in a neighborhood of the linear interpolation. A new path is constructed by altering the linear interpolation using a novel interpretation of Reidemeister moves from knot theory working on three-dimensional curves rather than on knot diagrams. Either the algorithm finds a self-avoiding path or it returns a smallest set of essential self-intersections. Each of these indicates a significant difference between the folds of the aligned protein structures. As expected, we find at least one essential self-intersection separating most unknotted structures from a knotted structure, and we find even larger motions in proteins connected by obstruction free linear interpolations. We also find examples of homologous proteins that are differently threaded, and we find many distinct folds connected by longer but simple deformations. TM-align is one of the most restrictive alignment programs. With standard parameters, it only aligns residues superimposed within 5 Ångström distance. We find 42165 topological obstructions between aligned parts in 142068 TM-alignments. Thus, this restrictive alignment procedure still allows topological dissimilarity of the aligned parts. CONCLUSIONS Based on the data we conclude that our program ProteinAlignmentObstruction provides significant additional information to alignment scores based solely on distances between aligned and superimposed residue pairs.
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Abstract
For two decades, Rosetta has consistently been at the forefront of protein structure
prediction. While it has become a very large package comprising programs, scripts, and tools, for
different types of macromolecular modelling such as ligand docking, protein-protein docking,
protein design, and loop modelling, it started as the implementation of an algorithm for ab initio
protein structure prediction. The term ’Rosetta’ appeared for the first time twenty years ago in the
literature to describe that algorithm and its contribution to the third edition of the community wide
Critical Assessment of techniques for protein Structure Prediction (CASP3). Similar to the Rosetta
stone that allowed deciphering the ancient Egyptian civilisation, David Baker and his co-workers
have been contributing to deciphering ’the second half of the genetic code’. Although the focus of
Baker’s team has expended to de novo protein design in the past few years, Rosetta’s ‘fame’ is
associated with its fragment-assembly protein structure prediction approach. Following a
presentation of the main concepts underpinning its foundation, especially sequence-structure
correlation and usage of fragments, we review the main stages of its developments and highlight
the milestones it has achieved in terms of protein structure prediction, particularly in CASP.
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Affiliation(s)
- Jad Abbass
- Department of Computer Science, Lebanese International University, Bekaa, Lebanon
| | - Jean-Christophe Nebel
- Faculty of Science, Engineering and Computing, Kingston University, London, KT1 2EE, United Kingdom
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McFarlane JMB, Krause KD, Paci I. Accelerated Structural Prediction of Flexible Protein–Ligand Complexes: The SLICE Method. J Chem Inf Model 2019; 59:5263-5275. [DOI: 10.1021/acs.jcim.9b00688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- James M. B. McFarlane
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Katherine D. Krause
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Irina Paci
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
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Ozgur B, Ozdemir ES, Gursoy A, Keskin O. Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations. J Phys Chem B 2017; 121:3686-3700. [DOI: 10.1021/acs.jpcb.6b10401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Beytullah Ozgur
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - E. Sila Ozdemir
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
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Perez A, Morrone JA, Brini E, MacCallum JL, Dill KA. Blind protein structure prediction using accelerated free-energy simulations. SCIENCE ADVANCES 2016; 2:e1601274. [PMID: 27847872 PMCID: PMC5106196 DOI: 10.1126/sciadv.1601274] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/07/2016] [Indexed: 05/30/2023]
Abstract
We report a key proof of principle of a new acceleration method [Modeling Employing Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. It shows that such Boltzmann-satisfying techniques are now sufficiently fast and accurate to predict native protein structures in a limited test within the Critical Assessment of Structure Prediction (CASP) community-wide blind competition.
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Affiliation(s)
- Alberto Perez
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Joseph A. Morrone
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Emiliano Brini
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Justin L. MacCallum
- Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Physics Astronomy, Stony Brook University, Stony Brook, NY 11794, USA
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Kryshtafovych A, Monastyrskyy B, Fidelis K. CASP11 statistics and the prediction center evaluation system. Proteins 2016; 84 Suppl 1:15-9. [PMID: 26857434 PMCID: PMC5479680 DOI: 10.1002/prot.25005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/18/2016] [Accepted: 02/04/2016] [Indexed: 01/10/2023]
Abstract
We outline the role of the Protein Structure Prediction Center (predictioncenter.org) in conducting the CASP11 and CASP ROLL experiments, discuss the experiment statistics, and provide an overview of the present CASP infrastructure. The biggest changes compared to the previous CASPs are the implementation of the evaluation system incorporating practically all evaluation measures, statistical tests, and visualization tools historically used by the CASP assessors, the expansion of the infrastructure to incorporate new categories of contact-assisted and multimeric predictions, and the redesign of the assessors' web-workspace enabling assessments based on multiple measures for different group categories and target sets. Proteins 2016; 84(Suppl 1):15-19. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, 95616
| | - Bohdan Monastyrskyy
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, 95616
| | - Krzysztof Fidelis
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, 95616.
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Kim JI, Kwon J, Baek I, Na S. Steered molecular dynamics analysis of the role of cofilin in increasing the flexibility of actin filaments. Biophys Chem 2016; 218:27-35. [PMID: 27589672 DOI: 10.1016/j.bpc.2016.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 08/25/2016] [Accepted: 08/27/2016] [Indexed: 12/14/2022]
Abstract
Cofilin is one of the most essential regulatory proteins and participates in the process of disassembling actin filaments. Cofilin induces conformational changes to actin filaments, and both the bending and torsional rigidity of the filament. In this study, we investigate the effects of cofilin on the mechanical properties of actin filaments using computational methods. Three models defined by their number of bound cofilins are constructed using coarse-grained MARTINI force field, and they are then extended with steered molecular dynamics simulation. After obtaining the stress-strain curves of the models, we calculate their Young's moduli and other mechanical properties that have not yet been determined for actin filaments. We analyze the cause of the different behaviors of the three models based on their atomistic geometrical differences. Finally, it is demonstrated that cofilin binding causes changes in the distances, angles, and stabilities of the residues in actin filaments.
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Affiliation(s)
- Jae In Kim
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Republic of Korea
| | - Junpyo Kwon
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Republic of Korea
| | - Inchul Baek
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Republic of Korea.
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Abstract
Motivation: Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. Results: We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts’ intuitive assessment of computational models and provides information of practical usefulness of models. Availability and implementation:https://bitbucket.org/mjamroz/flexscore Contact:dkihara@purdue.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michal Jamroz
- Department of Chemistry, University of Warsaw, Warsaw, 02-093, Poland
| | - Andrzej Kolinski
- Department of Chemistry, University of Warsaw, Warsaw, 02-093, Poland
| | - Daisuke Kihara
- Department of Biological Sciences Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
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Kim JI, Kwon J, Baek I, Na S. Biophysical characterization of cofilin-induced extension–torsion coupling in actin filaments. J Biomech 2016; 49:1831-1835. [DOI: 10.1016/j.jbiomech.2016.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 04/15/2016] [Accepted: 04/18/2016] [Indexed: 11/27/2022]
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11
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Kim JI, Kwon J, Baek I, Park HS, Na S. Cofilin reduces the mechanical properties of actin filaments: approach with coarse-grained methods. Phys Chem Chem Phys 2015; 17:8148-58. [PMID: 25727245 DOI: 10.1039/c4cp06100d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An actin filament is an essential cytoskeleton protein in a cell. Various proteins bind to actin for cell functions such as migration, division, and shape control. ADF/cofilin is a protein that severs actin filaments and is related to their dynamics. Actin is known to have excellent mechanical properties. Binding cofilin reduces its mechanical properties, and is related to the severing process. In this research, we applied a coarse-grained molecular dynamics simulation (CGMD) method to obtain actin filaments and cofilin-bound actin (cofilactin) filaments. Using these two obtained models, we constructed an elastic network model-based structure and conducted a normal mode analysis. Based on the low-frequency normal modes of the filament structure, we applied the continuum beam theory to calculate the mechanical properties of the actin and cofilactin filaments. The CGMD method provided structurally accurate actin and cofilactin filaments in relation to the mechanical properties, which showed good agreement with the established experimental results.
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Affiliation(s)
- Jae In Kim
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Republic of Korea.
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12
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Carlsen M, Koehl P, Røgen P. On the importance of the distance measures used to train and test knowledge-based potentials for proteins. PLoS One 2014; 9:e109335. [PMID: 25411785 PMCID: PMC4239004 DOI: 10.1371/journal.pone.0109335] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 08/31/2014] [Indexed: 12/15/2022] Open
Abstract
Knowledge-based potentials are energy functions derived from the analysis of databases of protein structures and sequences. They can be divided into two classes. Potentials from the first class are based on a direct conversion of the distributions of some geometric properties observed in native protein structures into energy values, while potentials from the second class are trained to mimic quantitatively the geometric differences between incorrectly folded models and native structures. In this paper, we focus on the relationship between energy and geometry when training the second class of knowledge-based potentials. We assume that the difference in energy between a decoy structure and the corresponding native structure is linearly related to the distance between the two structures. We trained two distance-based knowledge-based potentials accordingly, one based on all inter-residue distances (PPD), while the other had the set of all distances filtered to reflect consistency in an ensemble of decoys (PPE). We tested four types of metric to characterize the distance between the decoy and the native structure, two based on extrinsic geometry (RMSD and GTD-TS*), and two based on intrinsic geometry (Q* and MT). The corresponding eight potentials were tested on a large collection of decoy sets. We found that it is usually better to train a potential using an intrinsic distance measure. We also found that PPE outperforms PPD, emphasizing the benefits of capturing consistent information in an ensemble. The relevance of these results for the design of knowledge-based potentials is discussed.
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Affiliation(s)
- Martin Carlsen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Patrice Koehl
- Department of Computer Science and Genome Center, University of California Davis, Davis, CA, United States of America
| | - Peter Røgen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
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Perez A, Roy A, Kasavajhala K, Wagaman A, Dill KA, MacCallum JL. Extracting representative structures from protein conformational ensembles. Proteins 2014; 82:2671-80. [PMID: 24975328 DOI: 10.1002/prot.24633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 06/13/2014] [Accepted: 06/18/2014] [Indexed: 02/06/2023]
Abstract
A large number of methods generate conformational ensembles of biomolecules. Often one structure is selected to be representative of the whole ensemble, usually by clustering and selecting the structure closest to the center of the most populated cluster. We find that this structure is not necessarily the best representation of the cluster and present here two computationally inexpensive averaging protocols that can systematically provide better representations of the system, which can be more directly compared with structures from X-ray crystallography. In practice, systematic errors in the generated conformational ensembles appear to limit the maximum improvement of averaging methods.
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Affiliation(s)
- Alberto Perez
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
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14
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Nugent T, Cozzetto D, Jones DT. Evaluation of predictions in the CASP10 model refinement category. Proteins 2014; 82 Suppl 2:98-111. [PMID: 23900810 PMCID: PMC4282348 DOI: 10.1002/prot.24377] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/19/2013] [Accepted: 06/28/2013] [Indexed: 12/24/2022]
Abstract
Here we report on the assessment results of the third experiment to evaluate the state of the art in protein model refinement, where participants were invited to improve the accuracy of initial protein models for 27 targets. Using an array of complementary evaluation measures, we find that five groups performed better than the naïve (null) method—a marked improvement over CASP9, although only three were significantly better. The leading groups also demonstrated the ability to consistently improve both backbone and side chain positioning, while other groups reliably enhanced other aspects of protein physicality. The top-ranked group succeeded in improving the backbone conformation in almost 90% of targets, suggesting a strategy that for the first time in CASP refinement is successful in a clear majority of cases. A number of issues remain unsolved: the majority of groups still fail to improve the quality of the starting models; even successful groups are only able to make modest improvements; and no prediction is more similar to the native structure than to the starting model. Successful refinement attempts also often go unrecognized, as suggested by the relatively larger improvements when predictions not submitted as model 1 are also considered. Proteins 2014; 82(Suppl 2):98–111.
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Affiliation(s)
- Timothy Nugent
- Department of Computer Science Bioinformatics Group, University College London, London, WC1E 6BT, United Kingdom
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Mariani V, Biasini M, Barbato A, Schwede T. lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics 2013; 29:2722-8. [PMID: 23986568 PMCID: PMC3799472 DOI: 10.1093/bioinformatics/btt473] [Citation(s) in RCA: 503] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Motivation: The assessment of protein structure prediction techniques requires objective criteria to measure the similarity between a computational model and the experimentally determined reference structure. Conventional similarity measures based on a global superposition of carbon α atoms are strongly influenced by domain motions and do not assess the accuracy of local atomic details in the model. Results: The Local Distance Difference Test (lDDT) is a superposition-free score that evaluates local distance differences of all atoms in a model, including validation of stereochemical plausibility. The reference can be a single structure, or an ensemble of equivalent structures. We demonstrate that lDDT is well suited to assess local model quality, even in the presence of domain movements, while maintaining good correlation with global measures. These properties make lDDT a robust tool for the automated assessment of structure prediction servers without manual intervention. Availability and implementation: Source code, binaries for Linux and MacOSX, and an interactive web server are available at http://swissmodel.expasy.org/lddt Contact:torsten.schwede@unibas.ch Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Valerio Mariani
- Biozentrum, Universität Basel, Klingelbergstrasse 50-70 and Computational Structural Biology, SIB Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
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