Structural Modeling of Nanobodies: A Benchmark of State-of-the-Art Artificial Intelligence Programs.

The number of applications for nanobodies is steadily expanding, positioning these molecules as fast-growing biologic products in the biotechnology market. Several of their applications require protein engineering, which in turn would greatly benefit from having a reliable structural model of the nanobody of interest. However, as with antibodies, the structural modeling of nanobodies is still a challenge.

NbThermo: a new thermostability database for nanobodies.

We present NbThermo-a first-in-class database that collects melting temperatures (Tm), amino acid sequences and several other categories of useful data for hundreds of nanobodies (Nbs), compiled from an extensive literature search. This so-far unique database currently contains up-to-date, manually curated data for 564 Nbs. It represents a contribution to efforts aimed at developing new algorithms for reliable Tm prediction to assist Nb engineering for a wide range of applications of these unique biomolecules.

Identifying Potential Molecular Targets in Fungi Based on (Dis)Similarities in Binding Site Architecture with Proteins of the Human Pharmacolome.

Invasive fungal infections represent a public health problem that worsens over the years with the increasing resistance to current antimycotic agents. Therefore, there is a compelling medical need of widening the antifungal drug repertoire, following different methods such as drug repositioning, identification and validation of new molecular targets and developing new inhibitors against these targets. In this work we developed a structure-based strategy for drug repositioning and new drug design, which can be applied to infectious fungi and other pathogens.

Assessment of Different Parameters on the Accuracy of Computational Alanine Scanning of Protein-Protein Complexes with the Molecular Mechanics/Generalized Born Surface Area Method.

Computational alanine scanning with the molecular mechanics generalized Born surface area (MM/GBSA) method constitutes a widely used approach for identifying critical residues at protein-protein interfaces. Despite its popularity, the MM/GBSA method still has certain drawbacks due to its dependence on many factors. Here, we performed a systematical study on the impact of four different parameters, namely, the internal dielectric constant, the generalized Born model, the entropic term, and the inclusion of structural waters on the accuracy of computational alanine scanning calculations with the MM/GBSA method.

Structural Insights into the Design of Synthetic Nanobody Libraries.

Single domain antibodies from camelids, or nanobodies, are a unique class of antibody fragments with several advantageous characteristics: small monomeric size, high stability and solubility and easy tailoring for multiple applications. Nanobodies are gaining increasing acceptance as diagnostic tools and promising therapeutic agents in cancer and other diseases. While most nanobodies are obtained from immunized animals of the camelid family, a few synthetic nanobody libraries constructed in recent years have shown the capability of generating high quality nanobodies in terms of affinity and stability.

Structure-based design and construction of a synthetic phage display nanobody library.

Objective: To design and construct a new synthetic nanobody library using a structure-based approach that seeks to maintain high protein stability and increase the number of functional variants within the combinatorial space of mutations.

Results: Synthetic nanobody (Nb) libraries are emerging as an attractive alternative to animal immunization for the selection of stable, high affinity Nbs. Two key features define a synthetic Nb library: framework selection and CDR design.

AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4.

AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force field for metalloproteins. AMDock integrates several external programs (Open Babel, PDB2PQR, AutoLigand, ADT scripts) to accurately prepare the input structure files and to optimally define the search space, offering several alternatives and different degrees of user supervision. For visualization of molecular structures, AMDock uses PyMOL, starting it automatically with several predefined visualization schemes to aid in setting up the box defining the search space and to visualize and analyze the docking results.

Protein surface roughness accounts for binding free energy of Plasmepsin II-ligand complexes.

The calculation of absolute binding affinities for protein-inhibitor complexes remains as one of the main challenges in computational structure-based ligand design. The present work explored the calculations of surface fractal dimension (as a measure of surface roughness) and the relationship with experimental binding free energies of Plasmepsin II complexes. Plasmepsin II is an attractive target for novel therapeutic compounds to treat malaria.