Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold

Authors: Francis Gaudreault, Jason Baardsnes, Yuliya Martynova, Aurore Dachon, Hervé Hogues, Christopher R. Corbeil, Enrico O. Purisima, Mélanie Arbour, Traian Sulea

Source: Frontiers in Molecular Biosciences, Vol 10 (2023)

Subject Terms: binding affinity, protein-protein docking, rigid backbone, DARPin, ProPOSE, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2023.1253689/full; https://doaj.org/toc/2296-889X

Access URL: https://doaj.org/article/5dc9754727cd4f4ca1eb1c8bc25787c2

Solvated interaction energy: from small-molecule to antibody drug design

Authors: Enrico O. Purisima, Christopher R. Corbeil, Francis Gaudreault, Wanlei Wei, Christophe Deprez, Traian Sulea

Source: Frontiers in Molecular Biosciences, Vol 10 (2023)

Subject Terms: binding affinity, solvation, protein-ligand interaction, scoring function, antibody affinity maturation, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2023.1210576/full; https://doaj.org/toc/2296-889X

Access URL: https://doaj.org/article/6af386baeb524da2aa8fe61f44a00bc2

Redesigning an antibody H3 loop by virtual screening of a small library of human germline-derived sequences

Authors: Christopher R. Corbeil, Mahder Seifu Manenda, Traian Sulea, Jason Baardsnes, Marie-Ève Picard, Hervé Hogues, Francis Gaudreault, Christophe Deprez, Rong Shi, Enrico O. Purisima

Source: Scientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/32593c24308a497ea7ce2a68ef263f47

Coevolved Canonical Loops Conformations of Single-Domain Antibodies: A Tale of Three Pockets Playing Musical Chairs

Authors: Francis Gaudreault, Christopher R. Corbeil, Enrico O. Purisima, Traian Sulea

Source: Frontiers in Immunology, Vol 13 (2022)

Subject Terms: single-domain antibody, CDR prediction, antibody design, canonical structure, structural determinants, sequence preferences, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2022.884132/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/bbcd9a5cf7074b938164d9054c77ca66

Binding symmetry and surface flexibility mediate antibody self-association

Authors: Joseph D. Schrag, Marie-Ève Picard, Francis Gaudreault, Louis-Patrick Gagnon, Jason Baardsnes, Mahder S. Manenda, Joey Sheff, Christophe Deprez, Cassio Baptista, Hervé Hogues, John F. Kelly, Enrico O. Purisima, Rong Shi, Traian Sulea

Source: mAbs, Vol 11, Iss 7, Pp 1300-1318 (2019)

Subject Terms: Aggregation, native folding, single point mutation, structure-aggregation relationship, prediction method, Therapeutics. Pharmacology, RM1-950, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://doaj.org/toc/1942-0862; https://doaj.org/toc/1942-0870

Access URL: https://doaj.org/article/ce79077ec94f4690a1f6d8fff8b9138a

Structure-based engineering of pH-dependent antibody binding for selective targeting of solid-tumor microenvironment

Authors: Traian Sulea, Nazanin Rohani, Jason Baardsnes, Christopher R. Corbeil, Christophe Deprez, Yuneivy Cepero-Donates, Alma Robert, Joseph D. Schrag, Marie Parat, Mélanie Duchesne, Maria L. Jaramillo, Enrico O. Purisima, John C. Zwaagstra

Source: mAbs, Vol 12, Iss 1 (2020)

Subject Terms: Virtual histidine scanning, acidic pH selectivity, cell binding, spheroid growth, tumor targeting, Therapeutics. Pharmacology, RM1-950, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://doaj.org/toc/1942-0862; https://doaj.org/toc/1942-0870

Access URL: https://doaj.org/article/f7e7bbaa010a45d39cfc5376757156e7

A map of human cancer signaling

Authors: Qinghua Cui, Yun Ma, Maria Jaramillo, Hamza Bari, Arif Awan, Song Yang, Simo Zhang, Lixue Liu, Meng Lu, Maureen O'Connor‐McCourt, Enrico O Purisima, Edwin Wang

Source: Molecular Systems Biology, Vol 3, Iss 1, Pp 1-13 (2007)

Subject Terms: cancer signaling, cancer‐signaling map, DNA methylation, gene mutation, oncogenesignaling dependence, signaling network, Biology (General), QH301-705.5, Medicine (General), R5-920

File Description: electronic resource

Relation: https://doaj.org/toc/1744-4292

Access URL: https://doaj.org/article/bb82f4b756454fc0b84d61d76e1c433d

Solvated Interaction Energy (SIE) for Scoring Protein–Ligand Binding Affinities. 2. Benchmark in the CSAR-2010 Scoring Exercise.

Authors: Traian Sulea¹, Qizhi Cui¹, Enrico O. Purisima¹

Source: Journal of Chemical Information & Modeling; Sep2011, Vol. 51 Issue 9, p2066-2081, 16p

Restoring Charge Asymmetry in Continuum Electrostatics Calculations of Hydration Free Energies.

Authors: Enrico O. Purisima¹, Traian Sulea¹

Source: Journal of Physical Chemistry B. Jun2009, Vol. 113 Issue 24, p8206-8209. 4p.

Subject Terms: *ASYMMETRY (Chemistry), *ELECTROSTATICS, *HYDRATION, *GIBBS' free energy, *SOLVATION, *SIMULATION methods & models, *POISSON'S equation, *BOUNDARY element methods

Prediction of SAMPL-1 Hydration Free Energies Using a Continuum Electrostatics-Dispersion Model†.

Authors: Traian Sulea¹, Duangporn Wanapun¹, Sheldon Dennis¹, Enrico O. Purisima¹

Source: Journal of Physical Chemistry B; Apr2009, Vol. 113 Issue 14, p4511-4520, 10p

Exploring Inhibitor Binding at the S′ Subsites of Cathepsin L.

Authors: Shafinaz F. Chowdhury, Lissa Joseph, S. Kumar, Shenoy Rajesh Tulsidas, Sathesh Bhat, Edmund Ziomek, Robert Ménard, J. Sivaraman, Enrico O. Purisima

Source: Journal of Medicinal Chemistry; Feb2008, Vol. 51 Issue 5, p1361-1368, 8p

Solvated Interaction Energy (SIE) for Scoring Protein−Ligand Binding Affinities. 1. Exploring the Parameter Space.

Authors: Marwen Naïm¹, Sathesh Bhat¹, Kathryn N. Rankin¹, Sheldon Dennis¹, Shafinaz F. Chowdhury¹, Imran Siddiqi¹, Piotr Drabik¹, Traian Sulea¹, Christopher I. Bayly¹, Araz Jakalian¹, Enrico O. Purisima¹

Source: Journal of Chemical Information & Modeling; Jan2007, Vol. 47 Issue 1, p122-133, 12p

Bridging structural biology and genetics by computational methods: An investigation into how the R774C mutation in the AR gene can result in complete androgen insensitivity syndrome(Richard G. H. Cotton).

Authors: Jian Hui Wu, Bruce Gottlieb, Gerald Batist, Traian Sulea, Enrico O. Purisima, Lenore K. Beitel

Source: Human Mutation; Dec2003, Vol. 22 Issue 6, p465-475, 11p

Subject Terms: GENETIC mutation, ANDROGEN-insensitivity syndrome, SYNDROMES, GENES, MOLECULAR dynamics

On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations.

Authors: Kathryn N. Rankin, Traian Sulea, Enrico O. Purisima

Source: Journal of Computational Chemistry; 2003, Vol. 24 Issue 8, p954-962, 9p

Assisted Design of Antibody and Protein Therapeutics (ADAPT).

Authors: Victor Vivcharuk, Jason Baardsnes, Christophe Deprez, Traian Sulea, Maria Jaramillo, Christopher R Corbeil, Alaka Mullick, Joanne Magoon, Anne Marcil, Yves Durocher, Maureen D O'Connor-McCourt, Enrico O Purisima

Source: PLoS ONE, Vol 12, Iss 7, p e0181490 (2017)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5531539?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/eb1db71f334a418297760d9c820583f8

A Rational Engineering Strategy for Designing Protein A-Binding Camelid Single-Domain Antibodies.

Authors: Kevin A Henry, Traian Sulea, Henk van Faassen, Greg Hussack, Enrico O Purisima, C Roger MacKenzie, Mehdi Arbabi-Ghahroudi

Source: PLoS ONE, Vol 11, Iss 9, p e0163113 (2016)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5025174?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/2d1ae8285664432b857d78cf57c413ed