scholarly journals OCD.py - Characterizing immunoglobulin inter-domain orientations

2021 ◽  
Author(s):  
Valentin J Hoerschinger ◽  
Monica L Fernandez-Quintero ◽  
Franz Waibl ◽  
Johannes Kraml ◽  
Alexander Bujotzek ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
T Cell Receptors ◽  
Reference Structure ◽  
Data Input ◽  
Coordinate Systems ◽  
Reference Coordinate System ◽  
Antibody Therapeutics ◽  
Variable Domains ◽  
Cylindrical Domains ◽  
Suitable Reference

Inter-domain orientations between immunoglobulin domains are important for the modeling and engineering of novel antibody therapeutics. Previous tools to describe these orientations are applicable only to the variable domains of antibodies and T-cell receptors. We present the 'Orientation of Cylindrical Domains (OCD)' tool, which employs a transferable approach to calculate inter-domain orientations for all immunoglobulin domains. Based on a reference structure, the OCD tool automatically builds a suitable reference coordinate system for each domain. Through alignment, the reference coordinate systems are transferred onto the sample to calculate six measures which fully characterize the inter-domain orientation. Availability and implementation: The OCD approach is implemented as a stand-alone Python script, OCD.py, which can handle multiple types of data input for the analysis of single structures and molecular dynamics trajectories alike. OCD.py is available at https://github.com/liedllab/OCD under MIT license.

2.2. Working Group 2: Conceptual Definitions of Reference Coordinate Systems for Earth Dynamics

1975 ◽  
Vol 26 ◽  
pp. 21-26
Keyword(s):  
Coordinate System ◽  
Working Group ◽  
General Character ◽  
Coordinate Systems ◽  
Reference Coordinate System ◽  
Group 2 ◽  
Definition Of ◽  
Earth Dynamics

An ideal definition of a reference coordinate system should meet the following general requirements:1. It should be as conceptually simple as possible, so its philosophy is well understood by the users.2. It should imply as few physical assumptions as possible. Wherever they are necessary, such assumptions should be of a very general character and, in particular, they should not be dependent upon astronomical and geophysical detailed theories.3. It should suggest a materialization that is dynamically stable and is accessible to observations with the required accuracy.

scholarly journals On the dynamics of some small structural motifs in rRNA upon ligand binding

2008 ◽  
Vol 73 (1) ◽  
pp. 41-53
Author(s):  
Aleksandra Rakic ◽  
Petar Mitrasinovic
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Binding Sites ◽  
De Novo ◽  
Reference Structure ◽  
Base Pairs ◽  
Rna Sequences ◽  
Conformational Model ◽  
Thermodynamic Variables ◽  
Dynamics Simulations

The present study characterizes using molecular dynamics simulations the behavior of the GAA (1186-1188) hairpin triloops with their closing c-g base pairs in large ribonucleoligand complexes (PDB IDs: 1njn, 1nwy, 1jzx). The relative energies of the motifs in the complexes with respect to that in the reference structure (unbound form of rRNA; PDB ID: 1njp) display the trends that agree with those of the conformational parameters reported in a previous study1 utilizing the de novo pseudotorsional (?,?) approach. The RNA regions around the actual RNA-ligand contacts, which experience the most substantial conformational changes upon formation of the complexes were identified. The thermodynamic parameters, based on a two-state conformational model of RNA sequences containing 15, 21 and 27 nucleotides in the immediate vicinity of the particular binding sites, were evaluated. From a more structural standpoint, the strain of a triloop, being far from the specific contacts and interacting primarily with other parts of the ribosome, was established as a structural feature which conforms to the trend of the average values of the thermodynamic variables corresponding to the three motifs defined by the 15-, 21- and 27-nucleotide sequences. From a more functional standpoint, RNA-ligand recognition is suggested to be presumably dictated by the types of ligands in the complexes.

scholarly journals Reference Coordinate System Requirements for Space Physics and Astronomy

1980 ◽  
Vol 56 ◽  
pp. 71-75
Author(s):  
J. D. Mulholland
Keyword(s):  
Boundary Conditions ◽  
Coordinate System ◽  
Space Physics ◽  
Coordinate Frame ◽  
Coordinate Systems ◽  
Reference Coordinate System ◽  
System Requirements ◽  
Internal Coherence ◽  
Earth Dynamics

AbstractChanges in reference coordinate systems have major implications well beyond the realm of Earth dynamics. Definitions that serve geodynamic convenience may cause considerable effects for other disciplines. After presenting some typical areas in which coordinate frame definitions are important, recommendations are given for criteria to be considered as boundary conditions in discussing changes. These cover such qualities as observability, complexity, stability, internal coherence and uniqueness.

2.3. Working Group 3: Practical Realization of the Reference Coordinate Systems

1975 ◽  
Vol 26 ◽  
pp. 27-38
Keyword(s):  
Coordinate System ◽  
Working Group ◽  
Fundamental Constants ◽  
Practical Realization ◽  
Coordinate Systems ◽  
Reference Coordinate System ◽  
Measuring Techniques ◽  
Group 3 ◽  
Computational Procedures ◽  
Better Than

For a reference coordinate system to be useful to Blarth dynamics it must clearly display the phenomena of interest in a systematic and unambiguous way, free of detailed assumptions. For a clear display, it is absolutely essential that the system be realized to an accuracy substantially better than has been obtained heretofore. This demands not only improved measuring techniques and instruments, but also precise specification of computational procedures, assumptions, fundamental constants, etc., and meticulous implementation.

scholarly journals Net charge of antibody complementarity-determining regions is a key predictor of specificity

2018 ◽  
Vol 31 (11) ◽  
pp. 409-418 ◽  
Author(s):  
Lilia A Rabia ◽  
Yulei Zhang ◽  
Seth D Ludwig ◽  
Mark C Julian ◽  
Peter M Tessier
Keyword(s):  
Strong Predictor ◽  
Clinical Stage ◽  
Antibody Specificity ◽  
Net Charge ◽  
Antibody Therapeutics ◽  
Variable Domains ◽  
Self Association ◽  
Complementarity Determining Regions ◽  
Antibody Function ◽  
Positively Charged

Abstract Specificity is one of the most important and complex properties that is central to both natural antibody function and therapeutic antibody efficacy. However, it has proven extremely challenging to define robust guidelines for predicting antibody specificity. Here we evaluated the physicochemical determinants of antibody specificity for multiple panels of antibodies, including >100 clinical-stage antibodies. Surprisingly, we find that the theoretical net charge of the complementarity-determining regions (CDRs) is a strong predictor of antibody specificity. Antibodies with positively charged CDRs have a much higher risk of low specificity than antibodies with negatively charged CDRs. Moreover, the charge of the entire set of six CDRs is a much better predictor of antibody specificity than the charge of individual CDRs, variable domains (VH or VL) or the entire variable fragment (Fv). The best indicators of antibody specificity in terms of CDR amino acid composition are reduced levels of arginine and lysine and increased levels of aspartic and glutamic acid. Interestingly, clinical-stage antibodies with negatively charged CDRs also have a lower risk for poor biophysical properties in general, including a reduced risk for high levels of self-association. These findings provide powerful guidelines for predicting antibody specificity and for identifying safe and potent antibody therapeutics.

scholarly journals On the Absolute Orientation of the Selenodetic Reference Frame

1981 ◽  
Vol 63 ◽  
pp. 281-286
Author(s):  
V. S. Kislyuk
Keyword(s):  
Coordinate System ◽  
Center Of Mass ◽  
The Moon ◽  
Coordinate Systems ◽  
Inertial Coordinate System ◽  
Reference Coordinate System ◽  
The Earth ◽  
Principal Axes ◽  
The Mean ◽  
Selection Of

The selection of selenodetic reference coordinate system is an important problem in astronomy and selenodesy. For the purposes of reduction of observations, planning and executing space missions to the Moon, it is necessary, in any case, to know the orientation of the adopted selenodetic reference system in respect to the inertial coordinate system.Let us introduce the following coordinate systems: C(ξc, ηc, ζc), the Cassini system which is defined by the Cassini laws of the Moon rotation;D(ξd, ηd, ζd), the dynamical coordinate system, whose axes coincide with the principal axes of inertia of the Moon;Q(ξq, ηq, ζq), the quasi-dynamical coordinate system connected with the mean direction to the Earth, which is shifted by 254" West and 75" North from the longest axis of the dynamical system (Williams et al., 1973);S(ξs, ηs, ζs), the selenodetic coordinate system, which is practically realized by the positions of the points on the Moon surface given in Catalogues;I(X,Y,Z), the space-fixed (inertial) coordinate system. All the systems are selenocentric with the exception of S(ξs, ηs, ζs On the whole, the origin of this system does not coincide with the center of mass of the Moon.

Reference Coordinate System Requirements for Geophysics

1975 ◽  
Vol 26 ◽  
pp. 87-92
Author(s):  
P. L. Bender
Keyword(s):  
Coordinate System ◽  
Polar Motion ◽  
Main Part ◽  
Measurement Techniques ◽  
Reference Points ◽  
Angular Motion ◽  
Coordinate Systems ◽  
Axis Of Rotation ◽  
The Earth ◽  
Fixed System

AbstractFive important geodynamical quantities which are closely linked are: 1) motions of points on the Earth’s surface; 2)polar motion; 3) changes in UT1-UTC; 4) nutation; and 5) motion of the geocenter. For each of these we expect to achieve measurements in the near future which have an accuracy of 1 to 3 cm or 0.3 to 1 milliarcsec.From a metrological point of view, one can say simply: “Measure each quantity against whichever coordinate system you can make the most accurate measurements with respect to”. I believe that this statement should serve as a guiding principle for the recommendations of the colloquium. However, it also is important that the coordinate systems help to provide a clear separation between the different phenomena of interest, and correspond closely to the conceptual definitions in terms of which geophysicists think about the phenomena.In any discussion of angular motion in space, both a “body-fixed” system and a “space-fixed” system are used. Some relevant types of coordinate systems, reference directions, or reference points which have been considered are: 1) celestial systems based on optical star catalogs, distant galaxies, radio source catalogs, or the Moon and inner planets; 2) the Earth’s axis of rotation, which defines a line through the Earth as well as a celestial reference direction; 3) the geocenter; and 4) “quasi-Earth-fixed” coordinate systems.When a geophysicists discusses UT1 and polar motion, he usually is thinking of the angular motion of the main part of the mantle with respect to an inertial frame and to the direction of the spin axis. Since the velocities of relative motion in most of the mantle are expectd to be extremely small, even if “substantial” deep convection is occurring, the conceptual “quasi-Earth-fixed” reference frame seems well defined. Methods for realizing a close approximation to this frame fortunately exist. Hopefully, this colloquium will recommend procedures for establishing and maintaining such a system for use in geodynamics. Motion of points on the Earth’s surface and of the geocenter can be measured against such a system with the full accuracy of the new techniques.The situation with respect to celestial reference frames is different. The various measurement techniques give changes in the orientation of the Earth, relative to different systems, so that we would like to know the relative motions of the systems in order to compare the results. However, there does not appear to be a need for defining any new system. Subjective figures of merit for the various system dependon both the accuracy with which measurements can be made against them and the degree to which they can be related to inertial systems.The main coordinate system requirement related to the 5 geodynamic quantities discussed in this talk is thus for the establishment and maintenance of a “quasi-Earth-fixed” coordinate system which closely approximates the motion of the main part of the mantle. Changes in the orientation of this system with respect to the various celestial systems can be determined by both the new and the conventional techniques, provided that some knowledge of changes in the local vertical is available. Changes in the axis of rotation and in the geocenter with respect to this system also can be obtained, as well as measurements of nutation.

Note on Selection of Coordinate Systems for Geodynamics

1975 ◽  
Vol 26 ◽  
pp. 395-407
Author(s):  
S. Henriksen
Keyword(s):  
Sea Level ◽  
The Other ◽  
Coordinate Systems ◽  
Mean Sea Level ◽  
The Earth ◽  
The One ◽  
Static Systems ◽  
Selection Of

The first question to be answered, in seeking coordinate systems for geodynamics, is: what is geodynamics? The answer is, of course, that geodynamics is that part of geophysics which is concerned with movements of the Earth, as opposed to geostatics which is the physics of the stationary Earth. But as far as we know, there is no stationary Earth – epur sic monere. So geodynamics is actually coextensive with geophysics, and coordinate systems suitable for the one should be suitable for the other. At the present time, there are not many coordinate systems, if any, that can be identified with a static Earth. Certainly the only coordinate of aeronomic (atmospheric) interest is the height, and this is usually either as geodynamic height or as pressure. In oceanology, the most important coordinate is depth, and this, like heights in the atmosphere, is expressed as metric depth from mean sea level, as geodynamic depth, or as pressure. Only for the earth do we find “static” systems in use, ana even here there is real question as to whether the systems are dynamic or static. So it would seem that our answer to the question, of what kind, of coordinate systems are we seeking, must be that we are looking for the same systems as are used in geophysics, and these systems are dynamic in nature already – that is, their definition involvestime.

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