Can template-based protein models guide the design of sequence fitness for enhanced thermal stability of single domain antibodies?

Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening

(2015) Hongying Du et al.   METHODS

Structural Analysis of Diheme Cytochrome c by Hydrogen–Deuterium Exchange Mass Spectrometry and Homology Modeling

(2014) Ying Zhang et al.   BIOCHEMISTRY

Deciphering key features in protein structures with the new ENDscript server

(2014) Xavier Robert et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Unrestrained Replica-Exchange Simulations Using Dynamic Walkers in Temperature Space for Protein Structure Refinement

(2014) Mark A. Olson et al.   PLoS One

Development and Evaluation of Single Domain Antibodies for Vaccinia and the L1 Antigen

(2014) Scott A. Walper 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

Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction

(2014) Kai Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Second antibody modeling assessment (AMA-II)

(2014) Juan C. Almagro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural and mutational analysis of a monomeric and dimeric form of a single domain antibody with implications for protein misfolding

(2014) Jade George et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Isolation and Epitope Mapping of Staphylococcal Enterotoxin B Single-Domain Antibodies

(2014) Kendrick Turner et al.   SENSORS

Are predicted protein structures of any value for binding site prediction and virtual ligand screening?

(2013) Jeffrey Skolnick et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models

(2013) Mark A. Olson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Contributions of the Complementarity Determining Regions to the Thermal Stability of a Single-Domain Antibody

(2013) Dan Zabetakis et al.   PLoS One

Structure refinement of protein model decoys requires accurate side-chain placement

(2013) Mark A. Olson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of 3D models for allergen research

(2013) Trevor D. Power et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP) - round x

(2013) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of template-based protein structure predictions in CASP10

(2013) Yuanpeng J. Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessing Predictors of Changes in Protein Stability upon Mutation Using Self-Consistency

(2012) Grant Thiltgen et al.   PLoS One

Isolation of a Highly Thermal Stable Lama Single Domain Antibody Specific for Staphylococcus aureus Enterotoxin B

(2011) Russell R Graef et al.   BMC BIOTECHNOLOGY

Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding

(2011) Michael S. Lee et al.   JOURNAL OF CHEMICAL PHYSICS

Biotechnological applications of recombinant single-domain antibody fragments

(2011) Ario de Marco   Microbial Cell Factories

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

Assessment of template based protein structure predictions in CASP9

(2011) Valerio Mariani et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Binding Kinetics of Antiricin Single Domain Antibodies and Improved Detection Using a B Chain Specific Binder

(2010) George P. Anderson et al.   ANALYTICAL CHEMISTRY

Performance of protein stability predictors

(2010) Sofia Khan et al.   HUMAN MUTATION

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange

(2010) Michael S. Lee et al.   Journal of Chemical Theory and Computation

Dali server: conservation mapping in 3D

(2010) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

Llama Single Domain Antibodies Specific for the 7 Botulinum Neurotoxin Serotypes as Heptaplex Immunoreagents

(2010) Jerry O. Conway et al.   PLoS One

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

(2010) Jian Zhang et al.   PLoS One

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

Development of Antiricin Single Domain Antibodies Toward Detection and Therapeutic Reagents

(2008) George P. Anderson et al.   ANALYTICAL CHEMISTRY

Single-domain antibodies as building blocks for novel therapeutics

(2008) D SAERENS et al.   CURRENT OPINION IN PHARMACOLOGY

The Trp-cage: optimizing the stability of a globular miniprotein

(2008) B. Barua et al.   PROTEIN ENGINEERING DESIGN & SELECTION

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

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

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE