Sebastian Kelm
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View article: Muscular Strategies for Correcting the Pelvic Position to Improve Posture—An Exploratory Study
Muscular Strategies for Correcting the Pelvic Position to Improve Posture—An Exploratory Study Open
The correction of postural weaknesses through the better positioning of the pelvis is an important approach in sports therapy and physiotherapy. The pelvic position in the sagittal plane is largely dependent on the muscular balance of the …
View article: Structural modeling of antibody variable regions using deep learning—progress and perspectives on drug discovery
Structural modeling of antibody variable regions using deep learning—progress and perspectives on drug discovery Open
AlphaFold2 has hallmarked a generational improvement in protein structure prediction. In particular, advances in antibody structure prediction have provided a highly translatable impact on drug discovery. Though AlphaFold2 laid the groundw…
View article: A computational method for predicting the aggregation propensity of IgG1 and IgG4(P) mAbs in common storage buffers
A computational method for predicting the aggregation propensity of IgG1 and IgG4(P) mAbs in common storage buffers Open
The propensity for some monoclonal antibodies (mAbs) to aggregate at physiological and manufacturing pH values can prevent their use as therapeutic molecules or delay time to market. Consequently, developability assessments are essential t…
View article: Corrigendum: Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations
Corrigendum: Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations Open
[This corrects the article DOI: 10.3389/fimmu.2022.884110.].
View article: Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations
Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations Open
We have carried out a long-timescale simulation study on crystal structures of nine antibody-antigen pairs, in antigen-bound and antibody-only forms, using molecular dynamics with enhanced sampling and an explicit water model to explore in…
View article: The Chemical Synthesis of Knob Domain Antibody Fragments
The Chemical Synthesis of Knob Domain Antibody Fragments Open
Cysteine-rich knob domains found in the ultralong complementarity determining regions of a subset of bovine antibodies are capable of functioning autonomously as 3-6 kDa peptides. While they can be expressed recombinantly in cellular syste…
View article: The chemical synthesis of knob domain antibody fragments
The chemical synthesis of knob domain antibody fragments Open
Cysteine-rich knob domains found in the ultralong complementarity determining regions of a subset of bovine antibodies, are capable of functioning autonomously as 3-6 kDa peptides. While they can be expressed recombinantly in cellular syst…
View article: Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist
Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist Open
View article: Co-evolutionary Distance Prediction for Flexibility Prediction
Co-evolutionary Distance Prediction for Flexibility Prediction Open
Co-evolution analysis can be used to accurately predict residue-residue contacts from multiple sequence alignments. The introduction of machine-learning techniques has enabled substantial improvements in precision and a shift from predicti…
View article: Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice Open
Most current analysis tools for antibody next-generation sequencing data work with primary sequence descriptors, leaving accompanying structural information unharnessed. We have used novel rapid methods to structurally characterize the com…
View article: Reconstruction of apo A2A receptor activation pathways reveal ligand-competent intermediates and state-dependent cholesterol hotspots
Reconstruction of apo A2A receptor activation pathways reveal ligand-competent intermediates and state-dependent cholesterol hotspots Open
View article: Structural Diversity of B-Cell Receptor Repertoires along the B-cell Differentiation Axis in Humans and Mice
Structural Diversity of B-Cell Receptor Repertoires along the B-cell Differentiation Axis in Humans and Mice Open
Most current analysis tools for antibody next-generation sequencing data work with primary sequence descriptors, leaving accompanying structural information unharnessed. We have used novel rapid methods to structurally characterize the par…
View article: Computational approaches to therapeutic antibody design: established methods and emerging trends
Computational approaches to therapeutic antibody design: established methods and emerging trends Open
Antibodies are proteins that recognize the molecular surfaces of potentially noxious molecules to mount an adaptive immune response or, in the case of autoimmune diseases, molecules that are part of healthy cells and tissues. Due to their …
View article: Electrostatic interactions modulate the differential aggregation propensities of IgG1 and IgG4P antibodies and inform charged residue substitutions for improved developability
Electrostatic interactions modulate the differential aggregation propensities of IgG1 and IgG4P antibodies and inform charged residue substitutions for improved developability Open
Native state aggregation is an important concern in the development of therapeutic antibodies. Enhanced knowledge of mAb native state aggregation mechanisms would permit sequence-based selection and design of therapeutic mAbs with improved…
View article: Filtering Next-Generation Sequencing of the Ig Gene Repertoire Data Using Antibody Structural Information
Filtering Next-Generation Sequencing of the Ig Gene Repertoire Data Using Antibody Structural Information Open
Next-generation sequencing of the Ig gene repertoire (Ig-seq) produces large volumes of information at the nucleotide sequence level. Such data have improved our understanding of immune systems across numerous species and have already been…
View article: SCALOP: sequence-based antibody canonical loop structure annotation
SCALOP: sequence-based antibody canonical loop structure annotation Open
Motivation Canonical forms of the antibody complementarity-determining regions (CDRs) were first described in 1987 and have been redefined on multiple occasions since. The canonical forms are often used to approximate the antibody binding …
View article: Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires
Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires Open
Abs are immune system proteins that recognize noxious molecules for elimination. Their sequence diversity and binding versatility have made Abs the primary class of biopharmaceuticals. Recently, it has become possible to query their immens…
View article: Structurally Mapping Antibody Repertoires
Structurally Mapping Antibody Repertoires Open
Every human possesses millions of distinct antibodies. It is now possible to analyze this diversity via next-generation sequencing of immunoglobulin genes (Ig-seq). This technique produces large volume sequence snapshots of B-cell r…
View article: Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR
Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR Open
Aiming at the design of an allosteric modulator of the neonatal Fc receptor (FcRn)-Immunoglobulin G (IgG) interaction, we developed a new methodology including NMR fragment screening, X-ray crystallography, and magic-angle-spinning (MAS) N…
View article: Observed Antibody Space: a resource for data mining next generation sequencing of antibody repertoires
Observed Antibody Space: a resource for data mining next generation sequencing of antibody repertoires Open
Antibodies are immune system proteins that recognize noxious molecules for elimination. Their sequence diversity and binding versatility have made antibodies the primary class of biopharmaceuticals. Recently it has become possible to query…
View article: Efficient Sampling for the Prediction of Long and Multidomain Protein Structures
Efficient Sampling for the Prediction of Long and Multidomain Protein Structures Open
View article: A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density
A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density Open
View article: Investigating Cotranslational Folding in Membrane Proteins using Fragment-Based Structure Prediction
Investigating Cotranslational Folding in Membrane Proteins using Fragment-Based Structure Prediction Open
View article: Sphinx: merging knowledge-based and<i>ab initio</i>approaches to improve protein loop prediction
Sphinx: merging knowledge-based and<i>ab initio</i>approaches to improve protein loop prediction Open
Motivation Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databas…
View article: Examining the Conservation of Kinks in Alpha Helices
Examining the Conservation of Kinks in Alpha Helices Open
Kinks are a structural feature of alpha-helices and many are known to have functional roles. Kinks have previously tended to be defined in a binary fashion. In this paper we have deliberately moved towards defining them on a continuum, whi…
View article: SAbPred: a structure-based antibody prediction server
SAbPred: a structure-based antibody prediction server Open
SAbPred is a server that makes predictions of the properties of antibodies focusing on their structures. Antibody informatics tools can help improve our understanding of immune responses to disease and aid in the design and engineering of …
View article: Length-independent structural similarities enrich the antibody CDR canonical class model
Length-independent structural similarities enrich the antibody CDR canonical class model Open
Complementarity-determining regions (CDRs) are antibody loops that make up the antigen binding site. Here, we show that all CDR types have structurally similar loops of different lengths. Based on these findings, we created length-independ…
View article: PANDDAs: multi-dataset methods for finding hits from fragment screening by X-ray crystallography
PANDDAs: multi-dataset methods for finding hits from fragment screening by X-ray crystallography Open