A first prototype of MoFvAb was implemented in 2012 with the help of experts from Accelrys. == Supplemental Material == Supplemental data for this article can be accessed on thepublisher’s website. == Funding == AB is funded by the Roche Postdoc Fellowship Program. == Recommendations == == Associated Data == This section collects any data citations, data availability statements, or supplementary materials included in this article. == Supplementary Materials ==. competitive all-atom root mean square deviation values in the order of 1.5 on different evaluation datasets consisting of both known and previously unpublished antibody crystal structures. Keywords:antibody structure, amino acid sidechain conformation, homology modeling, macromolecular modeling, protein domain orientation, protein engineering, protein structure prediction == Abbreviations == root mean square deviation Antibody Modeling Assessment == Introduction == Antibodies are proteins that form an integral part of the specific immune response due to their ability to engage extracellular pathogenic structures (or antigens) with high affinity and specificity. Based on the recombination of a limited repertoire of different variable region germline genes, followed by somatic hypermutation and B cell-mediated antigen-dependent affinity maturation, evolution has brought forth an ingenious mechanism that enables the organism to generate a practically unlimited number of different specificities in answer to almost any antigen that this immune system is usually confronted with.1-3The unique properties of antibodies have made them an important tool in diagnostic and biotechnological applications,4and, last but not least, an increasingly sought-after therapeutic modality, in particular in the field of oncology.5-7 In order to fulfill the desired drug profile, therapeutic antibodies are often heavily engineered. For example, modifications may be made to modulate target binding and pharmacokinetic properties, increase the degree of humanness, IFN-alphaA or address developability issues that might affect drug safety and shelf life.8-11Many of those tasks are enabled, or at least greatly facilitated, by structure-based considerations around the atomic level.12The large number of publicly available antibody crystal structures that have Eluxadoline been solved during the last 25 y is an indicator for the relevance of this class of proteins. As of April 2015, the structural antibody database SAbDab13counts 2025 entries, a number that is steadily increasing. The demand to accelerate and facilitate the rational design and engineering of antibody-based therapeutics has brought forth a multitude of computational methods aimed at supporting those tasks.12-16Among these computational methods is usually a number of homology modeling applications that have been tailored to exclusively generate atomistic models of the antigen-binding (Fv) region of antibodies,17-19a functionality that is meant to complement and relieve experimental structure elucidation by crystallography. Given the large number of available crystal structures that can serve as templates, antibody Fv homology modeling is usually justifiably considered a less challenging problem than general homology modeling of arbitrary proteins, where often only a single template structure of low homology is available. 20-22Considering that the overall structure of the Fv region is usually well comprehended and characterized,23the challenge in antibody homology modeling is to create a model that is sufficiently precise to form a sound basis for structure-based engineering and design, at a Eluxadoline level of resolution that rivals that of a crystal structure. The main obstacle in this regard is the fact that the specificity of the antibody is usually mediated by 6 antigen-binding loops (complementarity-determining regions, Eluxadoline CDRs) that are hyper-variable in sequence and length.24,25While 5 of these CDRs are Eluxadoline prone to adopt canonical conformations26-28that to a certain degree can be predicted directly from sequence, the third loop around the variable region of the heavy chain, CDR-H3, is known to form a unique conformation that, in the majority of the known complex structures, constitutes the key contributor to the antibody-antigen interaction. Due to the fact that CDR-H3 is usually by far the most variable of the 6 CDR loops, 29a template loop structure of acceptable homology is often not available. Predicting the conformation of CDR-H3 with acceptable accuracy is usually thus the key challenge in antibody homology modeling.19The situation is complicated further because the Fv region is composed of 2 separate immunoglobulin domains, the variable region of the heavy chain and the variable region of the light chain (VH and VL), with 3 CDRs distributed on each of the 2. The relative orientation of the 2 2.