Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction

Shen, Yimin; Maupetit, Julien; Derreumaux, Philippe; Tufféry, Pierre

doi:10.1021/ct500592m

Cited by 550 publications

(440 citation statements)

References 60 publications

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“…A few successful force fields are available today to treat proteins and combinations of macromolecular entities, such as the Martini or other models [14][15][16][17]. In the last decade, we have been developing the optimized potential for efficient protein structure prediction (OPEP) force field as a result of intensive modelling and validation studies [11,[18][19][20][21][22][23][24][25]. The molecular model is able to reproduce accurately the secondary and tertiary folding of proteins, intermolecular aggregations, internal stability and motions and so forth.…”

Section: Methods (A) Coupling Lattice Boltzmann and Molecular Dynamicsmentioning

confidence: 99%

“…Notably, H-bonds between backbone atoms are modelled by twoand four-body potentials, rather than Coulomb interactions, and the interactions between ion pairs were derived from all-atom PMF calculations. OPEP coupled to various sampling methods has been successful tested on many non-amyloid proteins, recovering experimental structures and thermodynamics properties, [21][22][23][24]28] and protein/protein complexes [25]. Applied to amyloid proteins, OPEP simulations were the first to predict various topologies, such as the β-barrels, that were later identified experimentally [29,30].…”

Section: Methods (A) Coupling Lattice Boltzmann and Molecular Dynamicsmentioning

confidence: 99%

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Multiscale simulation of molecular processes in cellular environments

Chiricotto

Sterpone

Derreumaux

et al. 2016

Phil. Trans. R. Soc. A.

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One contribution of 17 to a theme issue 'Multiscale modelling at the physics-chemistry-biology interface' . We describe the recent advances in studying biological systems via multiscale simulations. Our scheme is based on a coarse-grained representation of the macromolecules and a mesoscopic description of the solvent. The dual technique handles particles, the aqueous solvent and their mutual exchange of forces resulting in a stable and accurate methodology allowing biosystems of unprecedented size to be simulated.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

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Section: Methods (A) Coupling Lattice Boltzmann and Molecular Dynamicsmentioning

confidence: 99%

Section: Methods (A) Coupling Lattice Boltzmann and Molecular Dynamicsmentioning

confidence: 99%

Multiscale simulation of molecular processes in cellular environments

Chiricotto

Sterpone

Derreumaux

et al. 2016

Phil. Trans. R. Soc. A.

Self Cite

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“…De novo structure prediction of the peptides was done in silico using the PEP-FOLD server [36,37]. Membrane association modes of protein and peptide models where predicted using PPM [38].…”

Section: Structure Prediction and CD Deconvolutionmentioning

confidence: 99%

“…The peptide de novo structure was predicted in silico using the PEP-FOLD algorithm [36] (Additional file 3: Figure S2). The MOG-derived peptides, as well as the Influenza hemagglutinin peptide (IA mimic), were predicted to harbor β strands, whereas other MBPmimicking peptides (HSV mimic, EB mimic, and PA mimic) as well as the P2-derived peptide P2gbs, contained an α helix as the dominant predicted secondary structure.…”

Section: Myelin-derived or Myelin-mimicking Peptides Of Potential Relmentioning

confidence: 99%

Myelin-derived and putative molecular mimic peptides share structural properties in aqueous and membrane-like environments

Tuusa

Raasakka

Ruskamo

et al. 2017

Mult Scler Demyelinating Disord

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Background: Despite intense research, the causes of various neurological diseases remain enigmatic to date. A role for viral or bacterial infection and associated molecular mimicry has frequently been suggested in the etiology of neurological diseases, including demyelinating autoimmune disorders, such as multiple sclerosis. Pathogen mimics of myelin-derived autoimmune peptides have been described in the literature and shown to induce myelin autoimmune responses in animal models. Methods: We carried out a structural study on myelin-derived peptides, and mimics thereof from various pathogens, in aqueous and membrane-like environments, using conventional and synchrotron radiation circular dichroism spectroscopy. A total of 13 peptides from the literature were studied, and 290 circular dichroism spectra were analysed. In addition, peptide structure predictions and vesicle aggregation assays were performed.

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“…The MHCI allele's 3D structure was achieved from PatchDock algorithm stimulated by object recognition and segmentation techniques of image used in Computer Visualization. It tries to match two parts by selection one part and search for the matching one as complementary [51]. The FireDock server statements used for problem of refinement in protein-protein docking resolutions; The method at the same time targets the flexibility problem and scoring of solutions was produced by docking algorithms as fast rigid-body [52][53][54].…”

Section: Dockingmentioning

confidence: 99%

Immunoinformatics-Peptide Driven Vaccine and In silico Modeling for Duvenhage Rabies Virus Glycoprotein G

Albagi¹,

Ahmed²,

Gumaa³

et al. 2017

J Clin Cell Immunol

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IntroductionLyssa viruses are representing a serious public health problem, especially in developing countries by causing lethal encephalitis in animals and humans. There is very few information on the way that lyssa viruses in general and Duvenhage virus caused disease [1]. This virus family has shape appear as a bullet, virion was envelop with a sense negatively RNA genome single strand which encodes for five proteins of viral: nucleoprotein, protein for matrix, phosphoprotein, glycoprotein and RNA-dependent RNA polymerase [2,3]. The incubation time is different, and the death is commonly occurred within six and eleven days after paralytic sign's forms, which limit treatment options [4]. Details of the lyssa virus's cycles like Duvenhage, Lagos bat, and Mokola viruses are unspecific [5,6]. The Lyssavirus genus of the family Rhabdoviridae consists of eleven additional virus species have been recognized within the genus Lyssavirus, which replicate in vertebrates, and mainly carried by bats except Mokola virus, and are restricted in special areas around the world [7]. African lyssa viruses include Mokola virus (MOKV), Lagos bat virus (LBV), and DUVV. European bat lyssa viruses 1 and 2 (EBLV 1 and 2 respectively), Irkut (IRKV), Aravan (ARAV), Khujant (KHUV) and West Caucasian bat virus (WCBV) cause cases in Europe and Asia. Australian bat Lyssavirus (ABLV) is restricted to Australia [8,9]. RABV (genotype 1) only bats isolated in South and North America, but rabies associated viruses have been bats isolated from another place. In Africa-countries, DUVV and LBV are bats associated with it, but Mokola virus is related with rodents and shrews [10]. Many susceptible vertebrates, sometimes have been found to be infected by rarely identified lyssaviruses, a human with Duvenhage virus [11,12]. The discovered of Duvenhage virus in South Africa in 1970 when the rabies was caused fatal like disease for a bitten person by a bat [13]. After that, they suggest that the virus isolated was a Miniopterusschreibersite for the reason that wide genus distribution in exposure area. The bat species previously identified as M. schreibersite in Africa is now known as Miniopterusnatalensis and then in 1986 the virus was isolated from an insectivorous bat, Nycteristhebaica in Zimbabwe. After 36 years later, DUVV was identified in human: in South Africa 2006 and subsequently in Kenya in 2007 [9]. Although most of the rabies infections are thought to be zoonotic, clinical cases have also been caused by Duvenhage virus, EBLV 1, EBLV 2, Australian bat Lyssavirus, Mokola virus and Irkut virus. Humans are likely to be susceptible to other rabies-related lyssa viruses [14]. Very few laboratories in African countries can diagnose species of rabies infection [9]. Some studies done to control measures and monitoring the spreading of lyssa viruses found that mongoose-related rabies in South Africa are different from classic rabies of dog [10]. Up to date no effective treatment is available for rabies infection. According to phylogeny, serological cro...

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Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction

Cited by 550 publications

References 60 publications

Multiscale simulation of molecular processes in cellular environments

Multiscale simulation of molecular processes in cellular environments

Myelin-derived and putative molecular mimic peptides share structural properties in aqueous and membrane-like environments

Immunoinformatics-Peptide Driven Vaccine and In silico Modeling for Duvenhage Rabies Virus Glycoprotein G

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