Search Results - "Loeffler, Johannes R"

Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties by Fernández-Quintero, Monica L, Loeffler, Johannes R, Kraml, Johannes, Kahler, Ursula, Kamenik, Anna S, Liedl, Klaus R

“…We present an approach to assess antibody CDR-H3 loops according to their dynamic properties using molecular dynamics simulations. We selected six antibodies…”
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Conformational selection of allergen-antibody complexes-surface plasticity of paratopes and epitopes by Fernández-Quintero, Monica L, Loeffler, Johannes R, Waibl, Franz, Kamenik, Anna S, Hofer, Florian, Liedl, Klaus R

“…Antibodies have the ability to bind various types of antigens and to recognize different antibody-binding sites (epitopes) of the same antigen with different…”
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T-Cell Receptor CDR3 Loop Conformations in Solution Shift the Relative Vα-Vβ Domain Distributions by Fernández-Quintero, Monica L, Pomarici, Nancy D, Loeffler, Johannes R, Seidler, Clarissa A, Liedl, Klaus R

“…T-cell receptors are an important part in the adaptive immune system as they are responsible for detecting foreign proteins presented by the major…”
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Inhibitors of Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) by Weiss, Alexander K H, Wurzer, Richard, Klapec, Patrycia, Eder, Manuel Philip, Loeffler, Johannes R, von Grafenstein, Susanne, Monteleone, Stefania, Liedl, Klaus R, Jansen-Dürr, Pidder, Gstach, Hubert

“…(FAHD1) acts as oxaloacetate decarboxylase in mitochondria, contributing to the regulation of the tricarboxylic acid cycle. Guided by a high-resolution X-ray…”
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Transitions of CDR-L3 Loop Canonical Cluster Conformations on the Micro-to-Millisecond Timescale by Fernández-Quintero, Monica L, Math, Barbara A, Loeffler, Johannes R, Liedl, Klaus R

“…Sequence and structural diversity of antibodies are concentrated on six hypervariable loops, also known as the complementarity determining regions (CDRs). Five…”
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Germline-Dependent Antibody Paratope States and Pairing Specific VH-VL Interface Dynamics by Fernández-Quintero, Monica L., Kroell, Katharina B., Bacher, Lisa M., Loeffler, Johannes R., Quoika, Patrick K., Georges, Guy, Bujotzek, Alexander, Kettenberger, Hubert, Liedl, Klaus R.

“…Antibodies have emerged as one of the fastest growing classes of biotherapeutic proteins. To improve the rational design of antibodies, we investigate the…”
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Local and Global Rigidification Upon Antibody Affinity Maturation by Fernández-Quintero, Monica L., Loeffler, Johannes R., Bacher, Lisa M., Waibl, Franz, Seidler, Clarissa A., Liedl, Klaus R.

“…During the affinity maturation process the immune system produces antibodies with higher specificity and activity through various rounds of somatic…”
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Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments by Fernández-Quintero, Monica L, Kroell, Katharina B, Heiss, Martin C, Loeffler, Johannes R, Quoika, Patrick K, Waibl, Franz, Bujotzek, Alexander, Moessner, Ekkehard, Georges, Guy, Liedl, Klaus R

“…Fab consist of a heavy and light chain and can be subdivided into a variable (V and V ) and a constant region (C 1 and C ). The variable region contains the…”
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Conformational Shifts of Stacked Heteroaromatics: Vacuum vs. Water Studied by Machine Learning by Loeffler, Johannes R, Fernández-Quintero, Monica L, Waibl, Franz, Quoika, Patrick K, Hofer, Florian, Schauperl, Michael, Liedl, Klaus R

“…Stacking interactions play a crucial role in drug design, as we can find aromatic cores or scaffolds in almost any available small molecule drug. To predict…”
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Comparing Antibody Interfaces to Inform Rational Design of New Antibody Formats by Fernández-Quintero, Monica L, Quoika, Patrick K, Wedl, Florian S, Seidler, Clarissa A, Kroell, Katharina B, Loeffler, Johannes R, Pomarici, Nancy D, Hoerschinger, Valentin J, Bujotzek, Alexander, Georges, Guy, Kettenberger, Hubert, Liedl, Klaus R

“…As the current biotherapeutic market is dominated by antibodies, the design of different antibody formats, like bispecific antibodies and other new formats,…”
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Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines by Fernández-Quintero, Monica L, Pomarici, Nancy D, Fischer, Anna-Lena M, Hoerschinger, Valentin J, Kroell, Katharina B, Riccabona, Jakob R, Kamenik, Anna S, Loeffler, Johannes R, Ferguson, James A, Perrett, Hailee R, Liedl, Klaus R, Han, Julianna, Ward, Andrew B

“…Antibodies and other new antibody-like formats have emerged as one of the most rapidly growing classes of biotherapeutic proteins. Understanding the structural…”
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Corrigendum: Comparing Antibody Interfaces to Inform Rational Design of New Antibody Formats by Fernández-Quintero, Monica L, Quoika, Patrick K, Wedl, Florian S, Seidler, Clarissa A, Kroell, Katharina B, Loeffler, Johannes R, Pomarici, Nancy D, Hoerschinger, Valentin J, Bujotzek, Alexander, Georges, Guy, Kettenberger, Hubert, Liedl, Klaus R

“…[This corrects the article DOI: 10.3389/fmolb.2022.812750.]…”
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Coil–Globule Transition Thermodynamics of Poly(N‑isopropylacrylamide) by Podewitz, Maren, Wang, Yin, Quoika, Patrick K, Loeffler, Johannes R, Schauperl, Michael, Liedl, Klaus R

“…Thermosensitive polymers such as poly­(N-isopropylacrylamide) (PNIPAM) undergo a phase transition in aqueous solution from a random-coil structural ensemble to…”
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Hydration of Aromatic Heterocycles as an Adversary of π‑Stacking by Loeffler, Johannes R, Schauperl, Michael, Liedl, Klaus R

“…Hydration is one of the key players in the protein–ligand binding process. It not only influences the binding process per se, but also the drug’s absorption,…”
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Thermosensitive Hydration of Four Acrylamide-Based Polymers in Coil and Globule Conformations by Quoika, Patrick K, Podewitz, Maren, Wang, Yin, Kamenik, Anna S, Loeffler, Johannes R, Liedl, Klaus R

“…To characterize the thermosensitive coil–globule transition in atomistic detail, the conformational dynamics of linear polymer chains of acrylamide-based…”
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CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis by Bruciaferri, Niccolo’, Eberhardt, Jerome, Llanos, Manuel A., Loeffler, Johannes R., Holcomb, Matthew, Fernandez-Quintero, Monica L., Santos-Martins, Diogo, Ward, Andrew B., Forli, Stefano

“…Cosolvent molecular dynamics (MDs) are an increasingly popular form of simulations where small molecule cosolvents are added to water-solvated protein systems…”
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STACKED - S olvation T heory of A romatic C omplexes as K ey for E stimating D rug Binding by Loeffler, Johannes R, Fernández-Quintero, Monica L, Schauperl, Michael, Liedl, Klaus R

“…The use of fragments to biophysically characterize a protein binding pocket and determine the strengths of certain interactions is a computationally and…”
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Paratope states in solution improve structure prediction and docking by Fernández-Quintero, Monica L., Vangone, Anna, Loeffler, Johannes R., Seidler, Clarissa A., Georges, Guy, Liedl, Klaus R.

“…Structure-based antibody design and accurate predictions of antibody-antigen interactions remain major challenges in computational biology. By using molecular…”
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The fumarylacetoacetate hydrolase (FAH) superfamily of enzymes: multifunctional enzymes from microbes to mitochondria by Weiss, Alexander K H, Loeffler, Johannes R, Liedl, Klaus R, Gstach, Hubert, Jansen-Dürr, Pidder

“…Prokaryotic and eukaryotic fumarylacetoacetate hydrolase (FAH) superfamily members, sharing conserved regions that form the so-called FAH-domain, catalyze a…”
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PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability by Hoerschinger, Valentin J, Waibl, Franz, Pomarici, Nancy D, Loeffler, Johannes R, Deane, Charlotte M, Georges, Guy, Kettenberger, Hubert, Fernández-Quintero, Monica L, Liedl, Klaus R

“…The electrostatic properties of proteins arise from the number and distribution of polar and charged residues. Electrostatic interactions in proteins play a…”
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