An integrated drug discovery software. MOE is able to track design ideas and ligand modifications with property models, produce correlation plots to visualize Structure, Property, Activity Relationships and visualize hydrophobic and charged protein surface to study aggregation prone regions. It can also automatically align and superpose antibody structures using the MOE Project protocol, generate and search advanced antibody queries with the Project Search application and build full length Ig structures including bispecifics with the Antibody Homology Modeler.
Offers an improved algorithm for complementarity determining region (CDR)-H3 modelling. WAM has been launched as an online modelling service. It constructs 3D models of antibody variable region fragments sequences using a combination of established theoretical methods together with the latest antibody structural information. The tool can generate auto-alignment but, if sequence contains non-standard features, a manual alignment is required.
Aims to optimize drug discovery process. BIOVIA Discovery Studio is a comprehensive suite of science applications. It offers a visualization and collaboration framework that includes a comprehensive science portfolio. It provides several tools for simulations, for macromolecule design and analysis, for antibody development, for structure-based design (SBD), for fragment-based design (FBD) or for pharmacophore and ligand-based design.
Obtains structural models of antibody fragments. ABGEN utilizes a homology based scaffolding technique, and includes the use of invariant and strictly conserved residue replacements and key inter-residue interactions. It can predict antigen binding fragments structures of anti-sweetener antibodies prior to crystallographic determinations. The tool provides a rapid, accurate, and easy-to-use modeling of antibody variable region fragments regions.
Constructs antibody models by simulating the natural evolution of antibody generation and affinity maturation. OptMAVEn can reduce the potent immunogenicity of designed antibody models and optimize their binding affinity to an antigen. It enables to (1) locate antigens in the antibody-binding site, (2) rediscover native antibody parts, (3) recapitulate known interactions responsible for affinity maturation and (4) unambiguously distinguish human antibody sequences from other species.
Predicts and analyzes combination antibody neutralization scores using IC50 and/or IC80 for individual antibodies. CombiNaber is a web-tool that predict bnAb combination neutralization results from single bnAb neutralization data using either “Bliss-Hill” (BH) or additive models and perform systematic analysis. It provides the user with the best candidate combinations for their panel. The predicted scores are systematically compared for all single antibodies and 2, 3 and 4 antibody combinations analyzed.
Takes an input antibody sequence and returns an energy optimized accurate structure in minutes. SmrtMolAntibody is part of a suite of modeling tools provided by Macromoltek. It creates a structure of an antibody from an individual sequence. The tool was improved with sequences for eleven Fvs and asked to produce structures of each of the antibody sequences. In 10 of 11 cases, the results using SmrtMolAntibody show good agreement between the submitted models and X-ray crystal structures.