I generally prefer to create software that has web-presence for facile reuse (otherwise why publish?). List of software directly relating to my drug-design work is below
- Protein Contact : data and resources to facilitate structural bioinformatics studies.
- Structural Antibody Database and Prediction Resources : currently used by leading pharmaceutical companies.
- Antibody Map : Collecting and annotating antibody repertoires.
- Antibody Structure : Collection of public resources on computaitonal tools for antibody design.
Below you can see a list of my publications, for citations please see Google Scholar:
- STCRDab: the structural T-cell receptor database,
J Leem, SHP de Oliveira, K Krawczyk, CM Deane (NAR 2017)
- In silico structural modeling of multiple epigenetic marks on DNA,
K Krawczyk, S Demharter, B Knapp, CM Deane, P Minary (Bioinformatics 2017)
- Computational tools for aiding rational antibody design,
K Krawczyk, J Dunbar, CM Deane (Computational Protein Design 2017)
- How B-cell receptor repertoire sequencing can be enriched with structural antibody data,
A Kovaltsuk, K Krawczyk, JD Galson, DF Kelly, CM Deane, J Trück (Frontiers in Immunology 2017)
- Tertiary element interaction in HIV-1 TAR,
K Krawczyk, AYL Sim, B Knapp, CM Deane, P Minary (J Chem Inf Model. 2016)
- SAbPred: a structure-based antibody prediction server,
J Dunbar, K Krawczyk, J Leem, C Marks, J Nowak, C Regep, G Georges, et al. (NAR 2016)
- Progress and challenges in predicting protein interfaces,
R Esmaielbeiki, K Krawczyk, B Knapp, JC Nebel, CM Deane (Briefings in Bioinformatics 2015)
- Improving B-cell epitope prediction and its application to global antibody-antigen docking,
K Krawczyk, X Liu, T Baker, J Shi, CM Deane (Bioinformatics 2014)
- SAbDab: the structural antibody database,
J Dunbar, K Krawczyk, J Leem, T Baker, A Fuchs, G Georges, J Shi, et al. (NAR 2013)
- Antibody i-Patch prediction of the antibody binding site improves rigid local antibody–antigen docking,
K Krawczyk, T Baker, J Shi, CM Deane (PEDS 2013)