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1.
Molecules ; 27(7)2022 Mar 24.
Artigo em Inglês | MEDLINE | ID: mdl-35408482

RESUMO

The SARS-CoV-2 virus, commonly known as COVID-19, first occurred in December 2019 in Wuhan, Hubei Province, China. Since then, it has become a tremendous threat to human health. With a pandemic threat, it is in the significant interest of the scientific world to establish its method of infection. In this manuscript, we combine knowledge of the infection mechanism with theoretical methods to answer the question of the virus's selectivity. We proposed a two-stage infection mechanism. In the first step, the virus interacts with the ACE2 receptor, with the "proper strength". When the interaction is too strong, the virus will remain in an "improper position"; if the interaction is too weak, the virus will "run away" from the cell. We also indicated three residues (positions 30, 31, and 353) located on the ACE2 protein-binding interface, which seems to be crucial for successful infection. Our results indicate that these residues are necessary for the initiation of the infection process.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Pandemias , Ligação Proteica , Glicoproteína da Espícula de Coronavírus/metabolismo
2.
Methods Mol Biol ; 2340: 79-104, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35167071

RESUMO

Protein aggregation is the cause of many, often lethal, diseases, including the Alzheimer's, Parkinson's, and Huntington's diseases, and familial amyloidosis. Theoretical investigation of the mechanism of this process, including the structures of the oligomeric intermediates which are the most toxic, is difficult because of long time scale of aggregation. Coarse-grained models, which enable us to extend the simulation time scale by three or more orders of magnitude, are, therefore, of great advantage in such studies. In this chapter, we describe the application of the physics-based UNited RESidue (UNRES) force field developed in our laboratory to study protein aggregation, in both free simulations and simulations of aggregation propagation from an existing template (seed), and illustrate it with the examples of Aß-peptide aggregation and Aß-peptide-assisted aggregation of the peptides derived from the repeat domains of tau (TauRD).


Assuntos
Agregados Proteicos , Proteínas , Simulação por Computador , Simulação de Dinâmica Molecular , Peptídeos , Conformação Proteica
3.
J Phys Chem B ; 126(3): 634-642, 2022 01 27.
Artigo em Inglês | MEDLINE | ID: mdl-35025490

RESUMO

One of the definitions of hydrophobic interactions is the aggregation of nonpolar particles in a polar solvent, such as water. While this phenomenon appears to be very simple, it is crucial for many complex processes, such as protein folding, to take place. In this work, the hydrophobic association of adamantane and hexane at various temperatures and ionic strengths was studied using molecular dynamics simulations with the AMBER 16.0 program and the GAFF force field. The potentials of mean force of hydrophobic dimer formation, as well as the excess free energy, excess energy, excess entropy, and excess heat capacity corresponding to the formation of the contact minimum, were determined and analyzed. For both systems, the depth of the contact minimum in the potential of mean force was found to increase with both temperature and ionic strength. The excess heat capacity of the association at the contact minimum and T = 298 K was found to be negative and to decrease, while the excess entropy and energy were found to be positive and to increase for both systems, the changes being more pronounced for the hexane dimer. The excess heat capacity is also greater in absolute value for the hexane dimer.


Assuntos
Adamantano , Hexanos , Interações Hidrofóbicas e Hidrofílicas , Solventes/química , Temperatura , Termodinâmica , Água/química
4.
Methods Mol Biol ; 2376: 399-416, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34845623

RESUMO

The physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics and its replica-exchange extensions, UNRES has found a variety of applications, including ab initio and database-assisted protein-structure prediction, simulating protein-folding pathways, exploring protein free-energy landscapes, and solving biological problems. This chapter provides a summary of UNRES and a guide for potential users regarding the application of the UNRES package in a variety of research tasks.


Assuntos
Conformação Proteica , Entropia , Simulação de Dinâmica Molecular , Dobramento de Proteína , Proteínas
5.
Biomolecules ; 11(9)2021 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-34572559

RESUMO

Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink's group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.


Assuntos
Modelos Teóricos , Simulação de Dinâmica Molecular , DNA/química , Hidrodinâmica , Ligação de Hidrogênio , Cinética , Proteínas Mutantes/química , Fosforilação , Dobramento de Proteína , Proteínas/química , Proteínas/metabolismo
6.
Matrix Biol Plus ; 12: 100081, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34505054

RESUMO

Syndecans are membrane proteoglycans regulating extracellular matrix assembly, cell adhesion and signaling. Their ectodomains can be shed from the cell surface, and act as paracrine and autocrine effectors or as competitors of full-length syndecans. We report the first biophysical characterization of the recombinant ectodomains of the four human syndecans using biophysical techniques, and show that they behave like flexible random-coil intrinsically disordered proteins, and adopt several conformation ensembles in solution. We have characterized their conformational landscapes using native mass spectrometry (MS) and ion-mobility MS, and demonstrated that the syndecan ectodomains explore the majority of their conformational landscape, from minor compact, globular-like, conformations to extended ones. We also report that the ectodomain of syndecan-4, corresponding to a natural isoform, is able to dimerize via a disulfide bond. We have generated a three-dimensional model of the C-terminus of this dimer, which supports the dimerization via a disulfide bond. Furthermore, we have mapped the NXIP adhesion motif of syndecans and their sequences involved in the formation of ternary complexes with integrins and growth factor receptors on the major conformations of their ectodomains, and shown that these sequences are not accessible in all the conformations, suggesting that only some of them are biologically active. Lastly, although the syndecan ectodomains have a far lower number of amino acid residues than their membrane partners, their intrinsic disorder and flexibility allow them to adopt extended conformations, which have roughly the same size as the cell surface receptors (e.g., integrins and growth factor receptors) they bind to.

7.
J Mol Graph Model ; 108: 108008, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34419932

RESUMO

The UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES-contact group), and (iii) template-assisted (the UNRES-template group). For most of the targets, the contact restraints were derived from the server models top-ranked by the DeepQA method, while the DNCON2 method was used for 11 targets. Our consensus-fragment procedure was used to run template-assisted predictions. Each group also processed the Nuclear Magnetic Resonance (NMR)- and Small Angle X-Ray Scattering (SAXS)-data assisted targets. The average Global Distance Test Total Score (GDT_TS) of the 'Model 1' predictions were 29.17, 39.32, and 56.37 for the UNRES, UNRES-contact, and UNRES-template predictions, respectively, increasing by 0.53, 2.24, and 3.76, respectively, compared to CASP13. It was also found that the GDT_TS of the UNRES models obtained in ab initio mode and in the contact-assisted mode decreases with the square root of chain length, while the exponent in this relationship is 0.20 for the UNRES-template group models and 0.11 for the best performing AlphaFold2 models, which suggests that incorporation of database information, which stems from protein evolution, brings in long-range correlations, thus enabling the correction of force-field inaccuracies.


Assuntos
Proteínas , Bases de Dados Factuais , Conformação Proteica , Espalhamento a Baixo Ângulo , Difração de Raios X
8.
J Comput Chem ; 42(29): 2054-2067, 2021 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-34402552

RESUMO

Pseudopotentials for the chemical cross-links comprising the glutamic- and aspartic-acid side chains bridged with adipic- (ADH) or pimelic-acid hydrazide (PDH), and the lysine side chains bridged with glutaric (BS2 G) or suberic acid (BS3 ) for coarse-grained cross-link-assisted simulations were determined by canonical molecular dynamics with the Amber14sb force field. The potentials depend on the distance between side-chain ends and on side-chain orientation, this preventing from making cross-link contacts across the globule in simulations. The potentials were implemented in the UNRES coarse-grained force field and their effect on the quality of models was assessed with 11 monomeric and 1 dimeric proteins, using synthetic or experimental cross-link data. Simulations with the new potentials resulted in improvement of the generated models compared to unrestrained simulations in more instances compared to those with the statistical potentials.


Assuntos
Modelos Moleculares , Proteínas/química , Conformação Proteica
9.
Proteins ; 89(12): 1800-1823, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34453465

RESUMO

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70-75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70-80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.


Assuntos
Biologia Computacional/métodos , Modelos Moleculares , Proteínas , Software , Sítios de Ligação , Simulação de Acoplamento Molecular , Domínios e Motivos de Interação entre Proteínas , Proteínas/química , Proteínas/metabolismo , Análise de Sequência de Proteína
10.
J Comput Chem ; 42(22): 1579-1589, 2021 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-34048074

RESUMO

A method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN ) protons, and the side-chain Hß protons, given the Cα -trace, have been derived and parameterized, by using the interproton distances calculated from a set of 140 high-resolution non-homologous protein structures. The mean standard deviation over all types of proton pairs in the set was 0.44 Å after fitting. Validation against a set of 41 proteins with NMR-determined structures, which were not considered in parameterization, resulted in average standard deviation from average proton-proton distances of the NMR-determined structures of 0.25 Å, compared to 0.21 Å obtained with the PULCHRA all-atom-chain reconstruction algorithm and to the 0.12 Å standard deviation of the average-structure proton-proton distance of NMR-determined ensembles. The formulas provide analytical forces and can, therefore, be used in coarse-grained molecular dynamics.


Assuntos
Ressonância Magnética Nuclear Biomolecular , Proteínas/análise , Modelos Moleculares
11.
Bioinformatics ; 37(11): 1613-1615, 2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-33079977

RESUMO

MOTIVATION: The majority of the proteins in living organisms occur as homo- or hetero-multimeric structures. Although there are many tools to predict the structures of single-chain proteins or protein complexes with small ligands, peptide-protein and protein-protein docking is more challenging. In this work, we utilized multiplexed replica-exchange molecular dynamics (MREMD) simulations with the physics-based heavily coarse-grained UNRES model, which provides more than a 1000-fold simulation speed-up compared with all-atom approaches to predict structures of protein complexes. RESULTS: We present a new protein-protein and peptide-protein docking functionality of the UNRES package, which includes a variable degree of conformational flexibility. UNRES-Dock protocol was tested on a set of 55 complexes with size from 43 to 587 amino-acid residues, showing that structures of the complexes can be predicted with good quality, if the sampling of the conformational space is sufficient, especially for flexible peptide-protein systems. The developed automatized protocol has been implemented in the standalone UNRES package and in the UNRES server. AVAILABILITY AND IMPLEMENTATION: UNRES server: http://unres-server.chem.ug.edu.pl; UNRES package and data used in testing of UNRES-Dock: http://unres.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Peptídeos , Proteínas , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Conformação Proteica
12.
Front Mol Biosci ; 8: 765562, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-35004845

RESUMO

Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this article, we review the recent developments in the concept and methods for the determination of the dynamic structures of flexible peptides and proteins. In particular, we describe ways to extract information from nuclear magnetic resonance small-angle X-ray scattering (SAXS), and chemical cross-linking coupled with mass spectroscopy (XL-MS) measurements. All these techniques can be used to obtain ensemble-averaged restraints or to re-weight the simulated conformational ensembles.

13.
Prog Mol Biol Transl Sci ; 170: 73-122, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32145953

RESUMO

In this chapter the scale-consistent approach to the derivation of coarse-grained force fields developed in our laboratory is presented, in which the effective energy function originates from the potential of mean force of the system under consideration and embeds atomistically detailed interactions in the resulting energy terms through use of Kubo's cluster-cumulant expansion, appropriate selection of the major degrees of freedom to be averaged out in the derivation of analytical approximations to the energy terms, and appropriate expression of the interaction energies at the all-atom level in these degrees of freedom. Our approach enables the developers to find correct functional forms of the effective coarse-grained energy terms, without having to import them from all-atom force fields or deriving them on a heuristic basis. In particular, the energy terms derived in such a way exhibit correct dependence on coarse-grained geometry, in particular on site orientation. Moreover, analytical formulas for the multibody (correlation) terms, which appear to be crucial for coarse-grained modeling of many of the regular structures such as, e.g., protein α-helices and ß-sheets, can be derived in a systematic way. Implementation of the developed theory to the UNIfied COarse-gRaiNed (UNICORN) model of biological macromolecules, which consists of the UNRES (for proteins), NARES-2P (for nucleic acids), and SUGRES-1P (for polysaccharides) components, and is being developed in our laboratory is described. Successful applications of UNICORN to the prediction of protein structure, simulating the folding and stability of proteins and nucleic acids, and solving biological problems are discussed.


Assuntos
Biopolímeros/química , Simulação de Dinâmica Molecular , DNA/química , Proteínas de Choque Térmico HSP70/química , Hidrodinâmica , Ligação de Hidrogênio , Cinética , Substâncias Macromoleculares/química , Ferramenta de Busca , Telômero/metabolismo , Termodinâmica
14.
Phys Chem Chem Phys ; 22(8): 4758-4771, 2020 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-32064469

RESUMO

The study provides a deep computational analysis of the thermodynamic and structural features associated with the hydration of xenon, Xe, and its pairwise hydrophobic interaction (i.e., the potential of mean force, PMF), over a large temperature range. Xe is described both as a Lennard-Jones particle, LJ-Xe, and as a Mie particle, Mie-Xe (pseudo hard sphere). Three different water models are used: TIP3P-Ew, SPCE and TIP4P-2005. Mie-Xe is more hydrophobic than LJ-Xe due to the lack of the attractive energetic interactions with water molecules; its hydration, around room temperature, is opposed by a large and negative entropy change and a positive enthalpy change. The PMF of Mie-Xe is characterized by a deep minimum at contact distance whose depth increases with temperature, and whose magnitude is significantly larger than that obtained for LJ-Xe. The contact minimum configuration of Mie-Xe is favoured by a large positive entropy change and contrasted by a positive enthalpy change. These results are qualitatively the same regardless of the water model used. There is no clear connection between the values determined for the thermodynamic functions and the structural features of the hydration shells surrounding the single Mie-Xe and the couple of Mie-Xe particles in the contact minimum configuration. This confirms that the structural reorganization of water associated with such processes is characterized by an almost complete enthalpy-entropy compensation.

15.
J Chem Phys ; 152(5): 054902, 2020 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-32035448

RESUMO

The force-matching approach to coarse graining, in which the forces that act on site centers are fitted to the respective average forces computed from all-atom molecular dynamics simulations, provides a link between coarse-grained and all-atom molecular dynamics. In the existing implementations, radial site-site interaction potentials are assumed, thus precluding extensive coarse-graining that usually requires anisotropic potentials. In this work, we extended the force-matching approach to coarse-grained models with axially symmetric sites and implemented it to the UNRES model of polypeptide chains developed in our laboratory, in which the only interaction sites are united peptide groups and united side chains, the α-carbon atoms serving as anchor points. The optimizable parameters were those of the UNRES energy function and not whole potential profiles, which provide better transferability. We tested the implementation with the 20-residue tryptophan-cage miniprotein, selected as the training protein, starting from the NEWCT-9P variant of UNRES. The reference forces were obtained from implicit- and explicit-solvent simulations. Using a target function composed of a force-matching term and a maximum-likelihood term that drives the force field at reproducing the NMR-determined conformational ensembles at three selected temperatures, force fields were obtained which did not produce site-site clashes for the structures simulated with all-atom molecular dynamics with AMBER, and modeled the structures of α-helical proteins with resolution comparable to that of the NEWCT-9P force field. The new force fields also produced the free-energy landscapes of tryptophan cage similar to those obtained from the all-atom molecular dynamics runs.


Assuntos
Simulação de Dinâmica Molecular , Proteínas/química , Ressonância Magnética Nuclear Biomolecular , Conformação Proteica
16.
J Chem Inf Model ; 60(3): 1844-1864, 2020 03 23.
Artigo em Inglês | MEDLINE | ID: mdl-31999919

RESUMO

The method for protein-structure prediction, which combines the physics-based coarse-grained UNRES force field with knowledge-based modeling, has been developed further and tested in the 13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP13). The method implements restraints from the consensus fragments common to server models. In this work, the server models to derive fragments have been chosen on the basis of quality assessment; a fully automatic fragment-selection procedure has been introduced, and Dynamic Fragment Assembly pseudopotentials have been fully implemented. The Global Distance Test Score (GDT_TS), averaged over our "Model 1" predictions, increased by over 10 units with respect to CASP12 for the free-modeling category to reach 40.82. Our "Model 1" predictions ranked 20 and 14 for all and free-modeling targets, respectively (upper 20.2% and 14.3% of all models submitted to CASP13 in these categories, respectively), compared to 27 (upper 21.1%) and 24 (upper 18.9%) in CASP12, respectively. For oligomeric targets, the Interface Patch Similarity (IPS) and Interface Contact Similarity (ICS) averaged over our best oligomer models increased from 0.28 to 0.36 and from 12.4 to 17.8, respectively, from CASP12 to CASP13, and top-ranking models of 2 targets (H0968 and T0997o) were obtained (none in CASP12). The improvement of our method in CASP13 over CASP12 was ascribed to the combined effect of the overall enhancement of server-model quality, our success in selecting server models and fragments to derive restraints, and improvements of the restraint and potential-energy functions.


Assuntos
Algoritmos , Proteínas , Biologia Computacional , Consenso , Modelos Moleculares , Conformação Proteica
18.
Proteins ; 87(12): 1283-1297, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31569265

RESUMO

With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemical crosslinks within the framework of the 13th meeting of Critical Assessment of Structure Prediction approaches. This largest-to-date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases. However, in a broader context, it also suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows.


Assuntos
Biologia Computacional/métodos , Reagentes para Ligações Cruzadas/química , Modelos Moleculares , Conformação Proteica , Proteínas/química , Algoritmos , Cromatografia Líquida , Modelos Químicos , Reprodutibilidade dos Testes , Espectrometria de Massas em Tandem
19.
Int J Mol Sci ; 20(20)2019 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-31658765

RESUMO

In this study, we characterize the interactions between the extracellular matrix protein, procollagen C-proteinase enhancer-1 (PCPE-1), and glycosaminoglycans (GAGs), which are linear anionic periodic polysaccharides. We applied molecular modeling approaches to build a structural model of full-length PCPE-1, which is not experimentally available, to predict GAG binding poses for various GAG lengths, types and sulfation patterns, and to determine the effect of calcium ions on the binding. The computational data are analyzed and discussed in the context of the experimental results previously obtained using surface plasmon resonance binding assays. We also provide experimental data on PCPE-1/GAG interactions obtained using inhibition assays with GAG oligosaccharides ranging from disaccharides to octadecasaccharides. Our results predict the localization of GAG-binding sites at the amino acid residue level onto PCPE-1 and is the first attempt to describe the effects of ions on protein-GAG binding using modeling approaches. In addition, this study allows us to get deeper insights into the in silico methodology challenges and limitations when applied to GAG-protein interactions.


Assuntos
Cálcio/química , Proteínas da Matriz Extracelular/química , Proteínas da Matriz Extracelular/metabolismo , Glicosaminoglicanos/química , Glicosaminoglicanos/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Íons , Modelos Moleculares , Simulação de Acoplamento Molecular , Conformação Proteica , Domínios e Motivos de Interação entre Proteínas
20.
Proteins ; 87(12): 1200-1221, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31612567

RESUMO

We present the results for CAPRI Round 46, the third joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight of the homo-oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher-order assemblies. These were more difficult to model, as their prediction mainly involved "ab-initio" docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance "gap" was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template-based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.


Assuntos
Biologia Computacional , Conformação Proteica , Proteínas/ultraestrutura , Software , Algoritmos , Sítios de Ligação/genética , Bases de Dados de Proteínas , Modelos Moleculares , Ligação Proteica/genética , Mapeamento de Interação de Proteínas , Proteínas/química , Proteínas/genética , Homologia Estrutural de Proteína
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