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How's idiotype different from paratope?

How's idiotype different from paratope?


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What I understand of these two terms is that:

Paratope is a portion of antibody that recognises and binds to specific antigen.

Idiotype is an antigenic determinant of antibody formed of CDRs that have specificity for a particular epitope. Some authors call the antibodies recognising a particular epitope an idiotype.

Well the CDRs, they actually form the paratope so is it right to say the CDR that acts as an paratope also forms the idiotypic determinant/ idiotype ?


I have read that the unique amino acid sequence of the VH and VL domains of a given antibody can function not only as an antigen-binding site but also as a set of antigenic determinants. the idiotypic determinants are generated by the confomation of the heavy- and light-chain variable region. Each individual antigenic determinant of the variable region is referred to as an idiotope. In some cases an idiotope may be the actual antigen-binding site (The paratope), and in some cases an idiotope may comprise variable region sequences OUTSIDE of the antigen-binding site. Therefore, each antibody will present multiple idiotopes, and the sum of the individual idiotopes is called the IDIOTYPE of the antibody.

I hope that had been helpful


The following was a reply by an expert from assignmentexpert.com :

Paratope is only the part of Ab that binds to the epitope of an antigen. But this does not mean that every amino acid in the CDR should bind to epitope - it is possible that only 1-2 AAs per CDR bind directly to epitope. Therefore, paratope is the part of the idiotype that binds to the epitope.


What is the Difference Between Epitope and Paratope

The main difference between epitope and paratope is that epitope is a specific antigenic determinant that occurs on the antigen, whereas paratope is the antigen-binding site on the antibody . Furthermore, immune system components, including antibodies, B cells, and T cells, recognize epitopes while paratope binds to the specific epitope.

Epitope and paratope are two types of binding regions found on proteins. They play an important function in the humoral immunity by means of recognition.

Key Areas Covered

Key Terms

Antibody, Antigen, Epitope, Humoral Immunity, Paratope


Isotypes, Allotypes, and Idiotypes

Human antibodies are Y-shaped, tetrapeptide glycoproteins made by two heavy chains and two light chains that are bound together by disulfide bonds. Like any other proteins, antibodies can act as an antigen, if injected into different species or hosts. For example, if antibodies from humans are injected into mice, mice will recognize these antibodies are foreign proteins (antigens) and will form antibodies against human antibodies (i.e. anti-human antibodies).

It is observed that the entire immunoglobulin is not immunogenic but it contains antigenic determinants at specific sites. Based on the location of those antigenic determinants, immunoglobulins are divided into, isotypes, allotypes, and idiotypes.

Isotypes

Each antibody has only one type of (γ, or α, or μ, or ε, or δ) heavy chain and one type of (k or λ) light chain. The structural differences in the constant region of a heavy chain or light chain determine immunoglobulin (Ig) class and sub-class, types and subtypes within a species. These constant region determinants are called isotypic determinants or isotypes.

Formation of anti-isotypic antibody

All members of a species carry the same constant-region genes (including multiple alleles) so when an antibody from one species is injected into another species, the isotypic determinants will be recognized as foreign, forming anti-isotypic antibody.

Allotypes

Although all members of a species inherit the same set of isotype genes, multiple alleles exist for some of the genes. These alleles encode subtle amino acid differences. Products of allelic forms of the same gene will have slightly different amino acid sequences in the constant regions, which are known as allotypic determinants. The sum of the individual allotypic determinants displayed by an antibody determines its allotype.

Allotypes in human

  1. Gamma-chain allotypes (also known as Gm markers): So far at least 25 different Gm allotypes have been identified e.g. G1m(1), G2m(23), G3m (11), G4m(4a).
  2. IgA2 subclass has 2 allotypes designated as A2m(1) and A2m(2).
  3. Kappa (κ) light chain has 3 allotypes, designated Km(1), Km(2), and Km(3).

Each of these allotypic determinants represents differences in one to four amino acids that are encoded by different alleles.

Formation of anti-allotypic antibodies

Antibody to allotypic determinants can be produced by injecting antibodies from one member of a species into another member of the same species who carries different allotypic determinants. Sometimes, a pregnant mother can produce antibodies to paternal allotypic determinants present on the fetal immunoglobulin. Anti-allotype antibodies may also be developed following blood transfusion.

Idiotype

Idiotype
Image source: Creative diagnostics

VH and VL domains of an antibody constitute an antigen-binding site. To recognize the vast array of antigens that a human can encounter in its lifetime, this variable region has different structural conformation owing to the presence of different amino acids. There are millions of such antibodies in the human body specific for each antigen.

These unique amino acid sequences present in the VH and VL domains of a given antibody also serves as a set of antigenic determinants. Each individual antigenic determinant of the variable region is referred to as an idiotope. Each antibody will present multiple idiotopes the sum of the individual idiotopes is called the idiotype of the antibody.


Variable region identical immunoglobulins differing in isotype express different paratopes

The finding that the antibody (Ab) constant (C) region can influence fine specificity suggests that isotype switching contributes to the generation of Ab diversity and idiotype restriction. Despite the centrality of this observation for diverse immunological effects such as vaccine responses, isotype-restricted antibody responses, and the origin of primary and secondary responses, the molecular mechanism(s) responsible for this phenomenon are not understood. In this study, we have taken a novel approach to the problem by probing the paratope with (15)N label peptide mimetics followed by NMR spectroscopy and fluorescence emission spectroscopy. Specifically, we have explored the hypothesis that the C region imposes conformational constraints on the variable (V) region to affect paratope structure in a V region identical IgG(1), IgG(2a), IgG(2b), and IgG(3) mAbs. The results reveal isotype-related differences in fluorescence emission spectroscopy and temperature-related differences in binding and cleavage of a peptide mimetic. We conclude that the C region can modify the V region structure to alter the Ab paratope, thus providing an explanation for how isotype can affect Ab specificity.


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In: Journal of Biological Chemistry , Vol. 287, No. 42, 12.10.2012, p. 35409-35417.

Research output : Contribution to journal › Article › peer-review

T1 - Variable region identical immunoglobulins differing in isotype express different paratopes

N2 - The finding that the antibody (Ab) constant (C) region can influence fine specificity suggests that isotype switching contributes to the generation of Ab diversity and idiotype restriction. Despite the centrality of this observation for diverse immunological effects such as vaccine responses, isotype-restricted antibody responses, and the origin of primary and secondary responses, the molecular mechanism(s) responsible for this phenomenon are not understood. In this study, we have taken a novel approach to the problem by probing the paratope with 15N label peptide mimetics followed by NMR spectroscopy and fluorescence emission spectroscopy. Specifically, we have explored the hypothesis that the C region imposes conformational constraints on the variable (V) region to affect paratope structure in a V region identical IgG1, IgG2a, IgG2b, and IgG3 mAbs. The results reveal isotype-related differences in fluorescence emission spectroscopy and temperature-related differences in binding and cleavage of a peptide mimetic. We conclude that the C region can modify the V region structure to alter the Ab paratope, thus providing an explanation for how isotype can affect Ab specificity.

AB - The finding that the antibody (Ab) constant (C) region can influence fine specificity suggests that isotype switching contributes to the generation of Ab diversity and idiotype restriction. Despite the centrality of this observation for diverse immunological effects such as vaccine responses, isotype-restricted antibody responses, and the origin of primary and secondary responses, the molecular mechanism(s) responsible for this phenomenon are not understood. In this study, we have taken a novel approach to the problem by probing the paratope with 15N label peptide mimetics followed by NMR spectroscopy and fluorescence emission spectroscopy. Specifically, we have explored the hypothesis that the C region imposes conformational constraints on the variable (V) region to affect paratope structure in a V region identical IgG1, IgG2a, IgG2b, and IgG3 mAbs. The results reveal isotype-related differences in fluorescence emission spectroscopy and temperature-related differences in binding and cleavage of a peptide mimetic. We conclude that the C region can modify the V region structure to alter the Ab paratope, thus providing an explanation for how isotype can affect Ab specificity.


NONCOMPETITIVE IMMUNOASSAY FOR SMALL MOLECULES

FORTÜNE KOHEN , . JOSEF DE BOEVER , in Immunoassay , 1996

5. CONCLUSIONS

In this chapter we have described the development of noncompetitive immunoassay procedures termed idiometric assays for small molecules as exemplified for estradiol and progesterone. The development of the idiometric assay has been achieved by the identification, production, and utilization of two types of anti-idiotypic antibodies induced by using the primary antibody as an immunogen. These anti-idiotypic antibodies identified as betatypes and alphatypes were selected by using a variety of screening procedures (see Figs. 19.2–19.5 ), and had the following characteristics:

5.1. Betatypes

These anti-idiotypic antibodies recognized an epitope at the unoccupied binding site (paratope). In addition, they were analyte sensitive and competed with the analyte for binding sites of the primary antibody. Indeed, the betatypes were used as labeled antigen in immunoassay procedures ( 11 ).

5.2. Alphatypes

These anti-idiotypic antibodies were selected on the basis that their epitopes were in close proximity to the paratope, and were unaffected by the presence or absence of the analyte. In particular, the alphatype identified for the idiometric assay could not bind to the primary antibody in the presence of the betatype due to steric hindrance (see Table 19.2 ).

The use of three matched antibodies (primary antibody, betatype, and alphatype) has enabled the development of a noncompetitive immunoassay method for small molecules (see Fig. 19.6 ). The method is an excess reagent assay, as shown by the calibration curves in Figs. 19.7 , 19.10 , and 19.11 . The addition of excess betatype does not displace the analyte and ensures a low background.

The idiometric assays for estradiol and progesterone demonstrate good sensitivity and precision when compared with conventional direct competitive immunoassays. Since the idiometric assay is an excess reagent method, it is highly suitable for dipstick technology. In addition, the endpoint is highly flexible. The markers, the primary antibody, or the alphatype can be labeled with enzymes, radioisotopes, or fluorescent or chemiluminescent tags. Currently, we are producing reagents for the development of idiometric assays for the measurement of urinary estrone-3-glucuronide and pregnanediol-3α-glucuronide. We are also investigating the suitability of this approach for measuring large molecules (e.g., growth hormone). Interestingly, the anti-idiotypes raised against anti-estradiol IgG have been shown to bind to the estrogen receptor ( 20 ). This finding suggests that there may be structural homology between the binding site environment of antibody and the receptor.


Abstract

At the turning point of the mid-80s much experimental work stands as evidence that Jerne's original network hypothesis may be correct. However, much of the available information stems from studies on regulation of idiotypes on antibodies/lymphocytes which recognize exogenous or synthetic antigens. By comparison, much less is known about regulation of autoimmunity through the idiotype of antibodies or receptors directed against self components. A distinction between antigens of external and internal origin is probably not just a problem of semantics self antigens may be regulated in a slightly different mode than are their non-self counterparts. Here Maurizio Zanetti discusses the need to analyse the immune response to self antigens independently.

This is publication number 73 from the Department of Immunology of the Medical Biology Institute, LaJolla, CA 92037. This work was supported in part by a Grant-in-Aid by QUIDEL, La Jolla, CA.


Ideotype Breeding: Frequently Asked Questions | Methods | Plant Breeding

Everything you need to know about ideotype breeding !

Ans. A biological mode which is expected to perform or behave in a predictable manner within a defined environment is known as ideotype. It is also known as ideal plant type or model plant type.

Q. 2. Who developed the concept of plant type?

Ans. The concept of plant type was first introduced in rice breeding by Jennings in 1964.

Q. 3. Who coined the term ideotype?

Ans. The term ideotype was coined by Donald in 1968 working with wheat crop.

Q. 4. What is crop ideotype?

Ans. A plant model which is expected to yield greater quantity of grains, fibre, oil or other useful product when developed as a cultivar is called crop ideotype.

Q. 5. Who developed the concept of crop ideotype?

Ans. The concept of crop ideotype was developed by Donald 1968 on wheat.

Q. 6. What is ideotype breeding?

Ans. A method of crop improvement which is used to enhance genetic yield potential through genetic manipulation of individual plant character is termed ideotype breeding.

Q. 7. What is harvest index?

Ans. The ratio of economic yield to the biological yield or the ratio of economic produce to total biomass is called harvest index.

Q. 8. Who coined the term harvest index?

Ans. The term harvest index was first used by Donald in 1962.

Q. 9. What is biological yield?

Ans. Total dry matter production per plant is called biological yield or biomass.

Q. 10. What is economic yield?

Ans. The dry weight of useful plant part such as grain yield in cereals, pulses and oilseeds and seed cotton yield in cotton is referred to as economic yield.

Q. 11. What is determinate plant type?

Ans. The plant type in which growth of apical bud is ceased after a definite period is known as determinate plant type. Usually such plants produce only one flush of flowers such as early genotypes of pigeon-pea, green-gram, black-gram, cowpea etc.

Q. 12. What are indeterminate plants?

Ans. Plant genotypes in which apical bud grows continuously are called indeterminate plants. Such genotypes can produce second flush of flowers such as long duration genotypes of cotton and pigeon-pea.

Q. 13. What is compact plant type?

Ans. Plant types which have erect stature and have very less plant spread are known as compact plant types also called erect plant types. Such plant types are suitable for closer spacing.

Q. 14. What is robust plant type?

Ans. Plant genotypes which have vigorous plant growth are called robust plant types. Such genotypes are generally spreading types.

Q. 15. What is dwarf plant type?

Ans. Plant genotype having dwarf stature is called dwarf plant type.

Q. 16. What is the source of dwarfing gene in wheat?

Ans. In wheat, Norin 10 is the important source of dwarfing gene.

Q. 17. What is the source of dwarfness in rice?

Ans. In rice, Dee-Geo-Woogen is the important source of dwarfing gene.

Q. 18. What is tall plant type?

Ans. Plant genotypes having tall stature are called tall plant types. Such genotypes are generally prone to lodging.

Q. 19. What is pyramidal plant type?

Ans. In dicots, genotypes having pyramidal shape such as in cotton refer to pyramidal plant type.

Q. 20. What are erect leaves?

Ans. In cereals, leaves having upright position are called erect leaves. Such leaves have acute angle with the stem and also have high CO2 fixation efficiency.

Q. 21. What are drooping leaves?

Ans. in cereals, leaves having downward bending position are known as drooping leaves. Such leaves have right or obtuse angle with the stem and are considered physiologically less efficient.

Q. 22. What are tillers?

Ans. In cereals, the replica of main stem originating from the base of a plant is called tiller.

Ans. In cereals, the shoot length from first internode to the base of the spike is called culm.

Q. 24. Define physiologically efficient plants.

Ans. Plant genotypes with following characteristics are considered physiologically efficient:

(i) High CO2 fixation efficiency.

(ii) High mineral absorption efficiency.

(iii) High response to nutrients.

(v) Photo and thermo insensitivity.

Q. 25. What is physiological crop breeding?

Ans. Genetic improvement of crop plants in relation to following physiological parameters is known as physiological crop breeding:

(i) CO2 fixation efficiency,

(ii) Nutrient uptake capacity,

(iv) Reduction in photo-respiration and transpiration.

Q. 26. What is synchronous maturity?

Ans. The maturity of all fruits of a plant at the same time is known as synchronous maturity. Such trait is desirable for harvesting by machine.

Q. 27. What is idiotype?

Ans. Morphological features of the chromosomes of a particular plant species refers to idiotype.

Q. 28. What are C3 plants?

Ans. Plant species producing three carbon compounds (phosphoglyceric acid) as the first stable substance during photosynthesis are called C3 plants. C3 plants are physiologically lesser efficient than C4 plants.

Q. 29. What are examples of C3 plants?

Ans. Majority of crop plants are C3. Examples of C3 plants include rice, wheat, barley, pulses, oil seeds etc.

Q. 30. What are C4 plants?

Ans. Those plant species which produce four carbon compounds (oxaloacetic acid) as the first stable product of photosynthesis are called C4 plants. Physiologically C4 plants are more efficient than C3 plants.

Q. 31. Cite examples of C4 plants.

Ans. C4 plants include Maize, Sorghum, Sugarcane and Amaranthus.

Q. 32. Who first proposed ideal plant type of maize?

Ans. In maize, ideal plant type was first suggested by Mock and Pearce in 1975.

Q. 33. Who first suggested ideal plant type of six-rowed barley?

Ans. In six-rowed barley, ideal plant type was first suggested by Rasmusson in 1987.

Q. 34. Who proposed ideal plant type of cotton for irrigated conditions?

Ans. The ideal plant type of American and Desi cottons for irrigated conditions was proposed by Singh et.al (1974).

Q. 35. Who proposed ideal plant type of cotton for rainfed conditions?

Ans. For rainfed conditions, ideal plant type of upland and arboreum cottons was proposed by Singh and Narayanan in 1993.

Q. 36. Who proposed ideotype of Brassica?

Ans. Ideotype of Brassica was proposed by Bhargava et al in 1984.

Q. 37. Who proposed ideotype of wheat for rainfed conditions?

Ans. In India, ideotype of wheat for rainfed conditions was proposed by R.D. Asana.

Q. 38. Who proposed ideotype of Brassica napus for rainfed conditions?

Ans. Ideotype of Brassica napus for rainfed conditions was proposed by Thurling in 1991.

Q. 39. What are main features of ideotype breeding?

Ans. Main features of ideotype breeding are given below:

(i) Emphasis is given on individual trait which enhances the yield.

(ii) It includes morphological and physiological traits.

(iii) It exploits physiological variation.

(iv) It involves inter-disciplining approach.

(v) It is a slow method of cultivar development.

(vi) Selection is focused a yield enhancing traits.

(vii) Values of each character are decided in advance.

Q. 40. What are main features of wheat ideotype?

Ans. Main features of wheat ideotype are listed below:

Q. 41. What are main features of rice ideotype?

Ans. Main features of rice ideotype as given below:

(ii) High tillering capacity,

(iii) Short, erect, thick and highly angled leaves.

Q. 42. What are main features of maize ideotype?

Ans. In maize, main features of ideal plant type are given below:

Q. 43. What are the factors affecting ideotype?

Ans. Ideotype is affected by following factors:

(ii) Type of cultivation or cultivation practices,

(iii) Socio­economic conditions of farmers,

(v) Market requirements etc.

Q. 44. What steps are involved in ideotype breeding?

Ans. Ideotype breeding consists of following steps:

(i) Development of conceptual model.

(ii) Selection of base material from germplasm.

(iii) Incorporation of desirable traits.

(iv) Selection of desirable plant type.

Q. 45. In which crops ideotype breeding has been rewarding?

Ans. Ideotype breeding has been rewarding in cereals (wheat and rice) and millets (Sorghum and pearl millet).

Q. 46. What is the plant type suggested by M.S. Swaminathan?

Ans. M.S. Swaminathan has listed the following desirable attributes of crop ideotypes with special reference to multiple cropping in the tropics and sub-tropics.

(i) Superior population performance.

(ii) High productivity per day.

(iii) High photosynthetic ability.

(v) Photo and thermo insensitivity.

(vi) High response to nutrients.

(vii) High productivity per unit of water.

(viii) Multiple resistances to insects and diseases.

(ix) Better protein quantity and quality.

(x) Crop canopy that can retain and fix a maximum of CO2.

(xi) Stability to mechanization.

Q. 47. What are advantages of ideotype breeding?

Ans. It provides solution to several problems at a time like disease, insects and lodging resistance, maturity duration, yield and quality by combining desirable genes for these traits from different sources into a single genotype.

Q. 48. What are demerits of ideotype breeding?

Ans. Ideotype breeding has some limitations or demerits. Incorporation of several morphological, physiological and resistance traits from different sources into a single genotype is a difficult task. Sometimes, combining of some characters is not possible due to tight linkage between desirable and undesirable characters. Presence of such linkage hinders the progress of ideotype breeding. Moreover, it is a slow method of cultivar development.

Q. 49. What are differences between traditional breeding and ideotype breeding?

Ans. Main differences between traditional breeding and ideotype breeding are presented below in Table 30.1:


Development and Characterization of a Neutralizing Anti-idiotype Antibody Against Mirvetuximab for Analysis of Clinical Samples

Antibody-drug-conjugates (ADCs) are an emerging class of biological therapeutics. Mirvetuximab soravtansine is a novel folate receptor alpha (FRα)-targeting ADC which represents a potential new treatment for patients with ovarian and other FRα-positive cancers. Since patient immune responses to biological therapeutics may negatively affect drug efficacy and patient safety, regulatory authorities require rigorous monitoring of patient samples. Taking advantage of the immune system’s ability to generate highly specific antibodies, the field has turned to anti-idiotype antibodies as powerful tools for the development of sensitive and specific bioassays. Here, we report the generation and characterization of a highly specific neutralizing anti-idiotype antibody directed against M9346A, the antibody moiety of mirvetuximab soravtansine. The anti-idiotype antibody recognizes M9346A with double-digit picomolar affinity, competes with folate receptor antigen for binding to M9346A, and can be used to develop both anti-drug-antibody and neutralizing antibody assays.

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Methods

Data retrieval and compilation

Coordinate files of Ab-Ag complexes were retrieved from RCSB PDB (www.rcsb.org/pdb). Data so obtained were filtered and subjected to mining as mentioned in the result section. CDRs were identified using Kabat numbering system [42]. Coordinate files of complexes were retrieved and segregated based on source of antibody into two groups, human and mouse. While more than 90% of the retrieved antibodies were obtained from immunized house mouse, the strain of the mouse was not considered as a criterion for selection of the antibodies as no two individuals have identical genetic make up, hence the immune repertoire would also vary.

Identification of germline origin of the antibodies and their clustering

Candidate sequences were queried for germline genes in IMGT Database using Ig BLAST tool 1.3.0 at NCBI with default settings [43, 44]. The antibodies were then clustered based on common germline VH origin. Data sharing no common origin, were discarded while the rest were grouped.

Structural analysis

Structure based sequence alignment of all the lineages were performed in Chimera 1.11.2 [45]. One antibody was randomly chosen as reference with which other structures were matched. RMSDs of CDRs were noted. Contacts between the complexes were noted from PDBsum [46]. For multi-subunit antigen, the bonds between antibody and each chain of the antigen are added and reported. In complexes where PDBsum did not fetch any interaction information, PISA 1.48 [47] was used to identify the contacts.

Selection of system

Three mature antibodies, anti-uPAR, Fab 5.11A1 and Fab ED10 that bound to uPAR, CD28 and DNA respectively of VH1–84 lineage from mouse formed a system (PDB ID: 3BT2, 1YJD, 2OK0 respectively). Two of four antibodies, Fab 10G5H6 bound with ectodomain D3 of IL-13 and antibody m66 bound with gp41 MPER (Membrane Proximal External Region) peptide (PDB ID: 4HWB, 4NRX respectively) of VH5–51 lineage from human comprised of the other system and were chosen for simulation. Since in human, the other 2 antibodies Fab 2558 and Fab CH58 also bound to peptides, therefore these were excluded in the study to maintain distinctness of epitope. Only molecules directly interacting with the antibody were retained, rest were deleted. For antibody, only Fv (fragment variable) region constituting of CDRs and framework regions was retained. Antigens from each of the complexes were removed to generate free form of antibodies.

Sequence analysis

Multiple sequence analysis of the antibodies and their corresponding germline VH-gene was performed online using CLUSTAL omega (default settings) because of accuracy of alignment [48]. Mutations were identified from the alignment. Percent identity matrix was generated from the alignment to obtain identity between the sequence with germline counterpart. Canonical classes of the CDRs were assigned using strict Chothia SDR templates (http://www.bioinf.org.uk/abs/chothia.html) [12, 31].

Molecular dynamics simulation

Simulation set-up

All the starting heteromeric structures were provided as input to tLEaP module in AMBER14 package to generate topology and coordinate files [49]. Molecular mechanics parameters were assigned using ff12SB force-field [50]. The molecules were explicitly solvated using TIP3P water box with box edges lying 10 Å from the outermost atoms of the proteins in all directions. Charge of the system was neutralized with monovalent counter ions, Na + or Cl-. Prior to subjecting to simulation, energy minimization was performed for 5000 steps with steepest descent for first 2500 steps followed by conjugate gradient for rest. If steric clashes persisted, minimization cycle was increased. Systems were heated to 300 K during a 14 ps dynamics simulation using the NVT ensemble. The temperature of the system was constrained using Langevin dynamics temperature coupling with a time step of 2 fs. Pressure was equilibrated to 1 atm over a period of 10 ps using isotropic position scaling keeping the temperature constant at 300 K. A third equilibration was run for 100 ps to stabilize the system. Production MD run was conducted using the NPT ensemble for 0.5 μs at 300 K and 1 atm for each system. Snapshots were saved at an interval of 10 ps. All the MD simulations were performed using Sander and a parallel CUDA version of PMEMD from AMBER14 [51, 52]. All simulations were performed in-house using High Performance Computing (HPC) facility with NVIDIA K20X GPUs.


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