Skip to content

Latest commit

 

History

History
108 lines (84 loc) · 9.82 KB

README.md

File metadata and controls

108 lines (84 loc) · 9.82 KB

A Collection of Platform, Tools, Resources and Companies for Antibody Engineering

Open Source Platforms / Models

Name Description PMID/GitHub
BioPhi A platform for antibody design, humanization, and humanness evaluation based on natural antibody repertoires and deep learning 35133949
DeepAb Deep learning models and structure realization scripts for the DeepAb antibody structure prediction method GitHub

Resources

Title Link
Computational and artificial intelligence-based methods for antibody development Link
Analysis of the antibody structure based on high-resolution crystallographic studies Link
Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies Link
Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery Link
Computational approaches to therapeutic antibody design: established methods and emerging trends Link
Efficient evolution of human antibodies from general protein language models Link

Technologies

Name Description PMID/Link
LIBRA-seq linking B cell receptor to antigen specificity through sequencing 31787378
BEAM Barcode Enabled Antigen Mapping Link

Tools

Tool Type Tool Name Description PMID/Link
Database Antibody Registry The Antibody Registry gives researchers a way to universally identify antibodies used in their research. Link
Database PDB Database of protein structures 10592235
Database OAS Compendium of Ig sequences gathered from large NGS studies 30217829
Database SAbDab Antibody structures in PDB 24214988
Database SAbDab-Thera Database of antibody therapeutics 31555805
Database IMGT Database on genome, proteome, genetics and structure of Ig, TCR and MHC 15608269
Database Abysis Database of sequence- and structure-based bioinformatics tools 27561707
Database Immune Epitope Database Database on antibody and T cell epitopes 30357391
Antibody Sequence Assessment Abnum Tool to number antibody VH and VL sequence 18614234
Antibody Sequence Assessment MUSCLE Tool for sequence alignment 15034147
Antibody Sequence Assessment CLUSTALW Tool for sequence alignment 12824352
Antibody Sequence Assessment Jalview Analysis and visualization of multiple sequence alignments 19151095
Antibody Sequence Assessment NetMHCIIpan Tool to predict binding sites of MHC II molecules 32308001
Antibody Sequence Assessment Therapeutic Antibody Profiler In silico assessment of antibody developability 30765520
Antibody Sequence Assessment Humanness Score Assess the degree of “humanness” of antibodies 17442342
Antibody Sequence Assessment Parapred Sequence-based algorithm for paratope prediction 29672675
Antibody Structural Assessment Swiss-model 3D modeling of antibodies 29788355
Antibody Structural Assessment PIGS 3D modeling of antibodies 25375991
Antibody Structural Assessment ABodyBuilder 3D modeling of antibodies 27392298
Antibody Structural Assessment PyMOL Molecular visualization and assessment 21053052
Antibody Structural Assessment SWISS PDBViewer Integrated suite of tools for structural assessment of proteins 19517507
Antibody Structural Assessment AbAngle Tool to compute relative orientation between the variable domains (VH and VL) 23708320
Protein-Protein Docking ZDOCK Protein-protein docking 12784371
Protein-Protein Docking HADDOCK Protein-protein docking 12580598
Protein-Protein Docking pyDockWeb Protein-protein docking 23661696
CDR Redesign AIF Distribution of pairwise contact in Ag-Ab interface 23569282
CDR Redesign EPCN 2D network of epitope-paratope contacts 26189681
CDR Redesign RosettaAntibodyDesign Framework for ab initio design of antibodies 29702641

Benchmarking

Name Description Link
Benchmarking of antibody modeling methods It contains the raw, intermediate and output data involved in the comparison of three tools of protein structure modelling from plain amino acid sequence. GitHub

Companies

Company Name Description Link
Natural Antibody Unlocking the power of data-driven predictive methods for antibody therapeutic industry. Link
Profluent Decoding the language of proteins with AI Link
BigHat Biosciences BigHat Biosciences is designing safer, more effective antibody therapies for patients using machine learning and synthetic biology. Link

Other Collections

Collection Name Description Link
Papers for protein design using deep learning Inspired by Kevin Kaichuang Yang's awesome Machine-learning-for-proteins, we established this repository with a sharper focus on deep learning for protein design, which is a rapidly evolving field. Link
Awesome BCR repertoire papers Collection of papers related to BCR repertoire analyses GitHub
Papers on machine learning for proteins A collaborative list of machine learning papers on protein applications. GitHub
Database Collection NAR Database Summary Paper Alphabetic List Link

中文资源

资源名称 链接
抗体发现:杂交瘤技术和噬菌体展示抗体库技术 Link
抗体筛选行业研究报告 Link
单克隆抗体 (科普) Link
LIBRA-seq是革命性的开发单克隆抗体的新方法 Link
用BEAM技术找单克隆抗体 Link
万字长文 >>> 深度解读抗体发现技术 http://thunder-bio.com/nd.jsp?id=61
抗体结构详解 http://www.detaibio.com/topics/antibody-structure.html