Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions

Ślusarz, Rafał; Lubecka, Emilia A.; Czaplewski, Cezary; Liwo, Adam

doi:10.3389/fmolb.2022.1071428

Cited by 3 publications

(4 citation statements)

References 83 publications

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“…The UNRES web server has also been developed, 172 which was extended to docking 173 and, recently, to handle data-assisted calculations. 174 2.5. Other Models.…”

Section: Sirahmentioning

confidence: 99%

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Pragmatic Coarse-Graining of Proteins: Models and Applications

Borges-Araújo,

Patmanidis,

Singh

et al. 2023

J. Chem. Theory Comput.

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The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.

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“…The UNRES web server has also been developed, 172 which was extended to docking 173 and, recently, to handle data-assisted calculations. 174 2.5. Other Models.…”

Section: Sirahmentioning

confidence: 99%

“…The UNRES package is available from the web page. The UNRES web server has also been developed, which was extended to docking and, recently, to handle data-assisted calculations …”

Section: Overview Of Pragmatic Cg Protein Modelsmentioning

confidence: 99%

Pragmatic Coarse-Graining of Proteins: Models and Applications

Borges-Araújo,

Patmanidis,

Singh

et al. 2023

J. Chem. Theory Comput.

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“…Because the cross-linking experiments are relatively fast and inexpensive, many molecular-modeling software packages use the cross-link information in data-assisted modeling of proteins, protein conformational ensembles, or protein complexes, , or for protein–peptide and protein–protein docking. ,− These packages are based on the existing software developed for modeling the structures of proteins or protein complexes such as XPLOR-NIH, ROSETTA, MEDUSA, I-TASSER, and UNRES, , or for protein docking, such as HADDOCK . Other software for cross-link-assisted protein docking have also been developed .…”

Section: Introductionmentioning

confidence: 99%

“…The potentials were determined by all-atom MD simulations of the respective model systems, and analytical expressions dependent on both distance and orientation of the side-chain ends were fitted to the obtained potentials of mean force. We implemented them in the coarse-grained UNRES model of polypeptide chains developed in our laboratory ,, and, later, in the UNRES web server . Because of substantial reduction of the number of interaction sites (only two sites per residue), UNRES is able to search the conformational space efficiently, providing an ∼1000-fold extension of the time-scale of simulations, compared to all-atom models .…”

Section: Introductionmentioning

confidence: 99%

Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures

Leśniewski,

Pyrka,

Czaplewski

et al. 2024

J. Chem. Inf. Model.

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The influence of distance restraints from chemical cross-link mass spectroscopy (XL-MS) on the quality of protein structures modeled with the coarse-grained UNRES force field was assessed by using a protocol based on multiplexed replica exchange molecular dynamics, in which both simulated and experimental cross-link restraints were employed, for 23 small proteins. Six cross-links with upper distance boundaries from 4 Å to 12 Å (azido benzoic acid succinimide (ABAS), triazidotriazine (TATA), succinimidyldiazirine (SDA), disuccinimidyl adipate (DSA), disuccinimidyl glutarate (DSG), and disuccinimidyl suberate (BS 3 )) and two types of restraining potentials ((i) simple flat-bottom Lorentz-like potentials dependent on side chain distance (all cross-links) and (ii) distance-and orientation-dependent potentials determined based on molecular dynamics simulations of model systems (DSA, DSG, BS 3 , and SDA)) were considered. The Lorentz-like potentials with properly set parameters were found to produce a greater number of higher-quality models compared to unrestrained simulations than the MD-based potentials, because the latter can force too long distances between side chains. Therefore, the flat-bottom Lorentz-like potentials are recommended to represent cross-link restraints. It was also found that significant improvement of model quality upon the introduction of cross-link restraints is obtained when the sum of differences of indices of cross-linked residues exceeds 150.

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Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution

Dziadek,

Sieradzan,

Czaplewski

et al. 2024

J. Chem. Theory Comput.

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In this paper, we evaluated the ability of four coarse-grained methods to predict protein flexible regions with potential biological importance, UNRES-flex, UNRES-DSSP-flex (based on the united residue model of polypeptide chains without and with secondary structure restraints, respectively), CABS-flex (based on the C-α, C-β, and side chain model), and nonlinear rigid block normal mode analysis (NOLB) with a set of 100 protein structures determined by NMR spectroscopy or X-ray crystallography, with all secondary structure types. End regions with high fluctuations were excluded from analysis. The Pearson and Spearman correlation coefficients were used to quantify the conformity between the calculated and experimental fluctuation profiles, the latter determined from NMR ensembles and X-ray B-factors, respectively. For X-ray structures (corresponding to proteins in a crowded environment), NOLB resulted in the best agreement between the predicted and experimental fluctuation profiles, while for NMR structures (corresponding to proteins in solution), the ranking of performance is CABS-flex > UNRES-DSSP-flex > UNRES-flex > NOLB; however, CABS-flex sometimes exaggerated the extent of small fluctuations, as opposed to UNRES-DSSP-flex.

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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions

Cited by 3 publications

References 83 publications

Pragmatic Coarse-Graining of Proteins: Models and Applications

Pragmatic Coarse-Graining of Proteins: Models and Applications

Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures

Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution

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