Machine Learning Feature Selection for Predicting High Concentration Therapeutic Antibody Aggregation

Five computational developability guidelines for therapeutic antibody profiling

(2019) Matthew I. J. Raybould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility

(2019) Aleksander Kuriata et al.   NUCLEIC ACIDS RESEARCH

Computational re-design of protein structures to improve solubility

(2019) Susanna Navarro et al.   Expert Opinion on Drug Discovery

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

Computational approaches to therapeutic antibody design: established methods and emerging trends

(2019) Richard A Norman et al.   BRIEFINGS IN BIOINFORMATICS

Selecting and engineering monoclonal antibodies with drug-like specificity

(2019) Charles G Starr et al.   CURRENT OPINION IN BIOTECHNOLOGY

Parapred: antibody paratope prediction using convolutional and recurrent neural networks

(2018) Edgar Liberis et al.   BIOINFORMATICS

Learned protein embeddings for machine learning

(2018) Kevin K Yang et al.   BIOINFORMATICS

How Well Do Low- and High-Concentration Protein Interactions Predict Solution Viscosities of Monoclonal Antibodies?

(2018) Mahlet A. Woldeyes et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Biophysical characterization and molecular simulation of electrostatically driven self-association of a single-chain antibody

(2018) Christopher J. O'Brien et al.   PROTEIN SCIENCE

In Silico Prediction of Diffusion Interaction Parameter (kD), a Key Indicator of Antibody Solution Behaviors

(2018) Dheeraj S. Tomar et al.   PHARMACEUTICAL RESEARCH

Antibody interface prediction with 3D Zernike descriptors and SVM

(2018) Sebastian Daberdaku et al.   BIOINFORMATICS

Deamidation and isomerization liability analysis of 131 clinical-stage antibodies

(2018) Xiaojun Lu et al.   mAbs

Prediction and Reduction of the Aggregation of Monoclonal Antibodies

(2017) Rob van der Kant et al.   JOURNAL OF MOLECULAR BIOLOGY

In-silico prediction of concentration-dependent viscosity curves for monoclonal antibody solutions

(2017) Dheeraj S. Tomar et al.   mAbs

Modeling and docking of antibody structures with Rosetta

(2017) Brian D Weitzner et al.   Nature Protocols

Biophysical properties of the clinical-stage antibody landscape

(2017) Tushar Jain et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid and accurate in silico solubility screening of a monoclonal antibody library

(2017) Pietro Sormanni et al.   Scientific Reports

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Interplay between the hydrophobic effect and dipole interactions in peptide aggregation at interfaces

(2016) Sai J. Ganesan et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Solubis: optimize your protein: Fig. 1.

(2015) Greet De Baets et al.   BIOINFORMATICS

The CamSol Method of Rational Design of Protein Mutants with Enhanced Solubility

(2015) Pietro Sormanni et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational tool for the early screening of monoclonal antibodies for their viscosities

(2015) Neeraj J Agrawal et al.   mAbs

Aggregation risk prediction for antibodies and its application to biotherapeutic development

(2015) Olga Obrezanova et al.   mAbs

Structure-Based Prediction of Asparagine and Aspartate Degradation Sites in Antibody Variable Regions

(2014) Jasmin F. Sydow et al.   PLoS One

Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization

(2014) Brian D. Weitzner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Weak Interactions Govern the Viscosity of Concentrated Antibody Solutions: High-Throughput Analysis Using the Diffusion Interaction Parameter

(2012) Brian D. Connolly et al.   BIOPHYSICAL JOURNAL

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Developability Index: A Rapid In Silico Tool for the Screening of Antibody Aggregation Propensity

(2011) Timothy M. Lauer et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Fragmentation of monoclonal antibodies

(2011) Josef Vlasak et al.   mAbs

Construction, MD Simulation, and Hydrodynamic Validation of an All-Atom Model of a Monoclonal IgG Antibody

(2010) J. Paul Brandt et al.   BIOPHYSICAL JOURNAL

Diffusion and Sedimentation Interaction Parameters for Measuring the Second Virial Coefficient and Their Utility as Predictors of Protein Aggregation

(2010) Atul Saluja et al.   BIOPHYSICAL JOURNAL

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PACKMOL: A package for building initial configurations for molecular dynamics simulations

(2009) L. Martínez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Design of therapeutic proteins with enhanced stability

(2009) N. Chennamsetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward high-resolution homology modeling of antibody Fvregions and application to antibody-antigen docking

(2008) Arvind Sivasubramanian et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS