Antibody structure prediction software tools | Immune system data analysis
Antibody engineering is a promising field for the treatment of diseases, including cancer, and inflammation. Antibody structure design is achieved with three-dimensional models from protein sequences, and permits the study of antibody properties such as stability, antigenicity, aggregation propensity, solubility and more. Antibody structure prediction software tools use amino-acid sequences to predict the structure of antibody variable regions, fir annotating antigen receptor variable domain sequences, and more.
Predicts the structure of an antibody variable region given the amino-acid sequences of the respective light and heavy chains. In an initial stage, RosettaAntibody identifies and displays the most sequence homologous template structures for the light and heavy framework regions and each of the complementarity determining region (CDR) loops. Subsequently, the most homologous templates are assembled into a side-chain optimized crude model, and the server returns a picture and coordinate file. For users requesting a high-resolution model, the server executes the full RosettaAntibody protocol which additionally models the hyper-variable CDR H3 loop.
A database search loop modelling algorithm. Its primary use is to fill in the gaps in incomplete 3D models of protein structures. The input is a 3D model of a protein structure as well as the location and amino acid sequence of the loop region to be modelled.
The binding site of an antibody is formed between the two variable domains, VH and VL, of its antigen binding fragment (Fab). ABangle allows the VH-VL orientation for any antibody to be automatically calculated and compared with all other known structures.
Provides a base for systematic analyses of expressed immune repertoires. DNAPLOT helps to detect patterns of changes in the complementary determining region (CDR) regions of a given repertoire. It permits to demonstrate the dynamics of an expressed repertoire. The tool allows to align V gene nucleotide sequences.
Is used in the de novo design of antibody binding pockets against specified antigen epitopes. OptCDR proposes a four-step procedure. First, canonical structures are selected for the six complementarity determining regions (CDRs). Next, the amino acid sequences of the selected structures are initialized. This is followed by several thousand iterations of the iterative protein redesign and optimization (IPRO) procedure to refine the backbones and amino acids of the CDRs. Finally, accumulating the most promising mutations generates a library of antibodies.
An antibody modeling pipeline that uses SAbDab knowledge-base of antibody structures to guide decision-making in modeling antibodies. ABodyBuilder can rapidly build accurate models of antibodies from sequence. Once a model has been generated, it can be downloaded by the user, or interactively analysed through a web server application. ABodyBuilder is a fully automated method for antibody model generation, making it ideal for challenges such as modeling large, next-generation sequencing (NGS) data sets. It can also model complete Fvs or nanobodies.
A web app for tertiary structural modeling of antibody variable regions. Kotai Antibody Builder constructs three-dimensional (3D) structures of antibody variable domains from sequence using canonical rules, new H3-rules and evolutionary information. This web app is a fully automated version of the semi-automated pipeline used successfully in the Second Antibody Modeling Assessment (AMA-II).