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Tremendous technological advances in peptide synthesis and modification in recent years have resolved the major limitations of peptide-based vaccines. B-cell epitopes are major components of these vaccines (besides having other biological applications). Researchers ha ...

In vaccine design, databases and in silico tools play different but complementary roles. Databases collect experimentally verified vaccines and vaccine components, and in silico tools provide computational methods to predict and design new vaccines and vaccine components. Vac ...

This minireview focuses on recent developments in the application of molecular dynamics to drug design. Recent applications of endpoint free-energy computational methods such as molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and generalized Born surface ar ...

Understanding structure–activity relationships (SARs) for a given set of molecules allows one to rationally explore chemical space and develop a chemical series optimizing multiple physicochemical and biological properties simultaneously, for instance, improving pot ...

Recent analysis on polypharmacology leads to the idea that only small fragments of drugs and targets are a key to understanding their interactions forming polypharmacology. This idea motivates us to build an in silico approach of finding significant substructure patterns from drug–t ...

Resistance to drugs that treat infectious disease is a major problem worldwide. The rapid emergence of drug resistance is not well understood. We present two in silico models for the discovery of drug resistance mechanisms and for combating the evolution of resistance, respectively. In the f ...

Essential genes are frequently conserved among bacterial species and thus microbial and eukaryote genome comparisons can be used to compile datasets of homologous proteins and families that can be utilized to identify attractive targets for the design of antimicrobial agents and ot ...

Classical antibiotic discovery efforts have relied mainly on molecular library screening coupled with target-based lead optimization. The conventional approaches are unable to tackle the emergence of antibiotic resistance and are failing to provide understanding of multi ...

Virtual screening has become a standard tool in drug discovery to identify novel lead compounds that target a biomolecule of interest. I present several concepts in ligand-based and structure-based virtual screening and discuss some of the current shortcomings and new developments. I a ...

The search for small molecules with activity against Mycobacterium tuberculosis increasingly uses �high-throughput screening and computational methods. Previously, we have analyzed recent studies in which computational tools were used for cheminformatics. We have now up ...

Computational simulations of essential biological systems in pathogenic organisms are increasingly being used to reveal structural and dynamical features for targets of interest. At the same time, increased research efforts, especially from academia, have been directed towa ...

Malaria, the disease caused by infection with protozoan parasites from the genus Plasmodium, claims the lives of nearly 1 million people annually. Developing nations, particularly in the African Region, bear the brunt of this malaria burden. Alarmingly, the most dangerous etiologic ag ...

This chapter reviews studies that have used in silico techniques to design or identify potential HIV-1 entry inhibitors targeting cellular receptors CD4, CCR5, and CXCR4 and envelope glycoproteins, gp120 and gp41 of HIV-1. Both structure- and ligand-based design techniques have been us ...

Anthrax is an acute infectious disease caused by the spore-forming, gram-positive, rod-shaped bacterium Bacillus anthracis. The anthrax toxin lethal factor (LF) is the primary anthrax toxin component responsible for cytotoxicity and host death and has been a heavily researched tar ...

This chapter explains techniques for recognition of nontrivial remote homology relationships involving proteins of Helicobacter pylori and their implications for function recognition. Using the remote homology detection method, employing multiple-profile repres ...

The broad goals of Collaborative Drug Discovery (CDD) are to enable a collaborative “cloud-based” tool to be used to bring together neglected disease researchers and other researchers from usually separate areas, to collaborate and to share compounds and drug discovery data in the resear ...

We present here an analytical protocol for the sensitive, specific, and accurate absolute quantification of cetuximab, a human:murine chimeric monoclonal antibody, using mass spectrometry. Extraction from human serum is performed with micrometric magnetized beads, functi ...

Surface plasmon resonance (SPR) is a key technology to evaluate IgG effector functions in vitro involving binding to Fcgamma receptors (FcγR). We describe here the chemical coupling of protein A to a sensor chip. IgGs prepared either from purified antibodies or from crude cell media supernat ...

One of the major issues for antibody treatment is enhancement of efficacy. Recent studies have highlighted the important role of effector functions in improvement of antibody therapy. Among effector functions, complement-dependent cytotoxicity (CDC), which induces cell lysis by a ...

In order to improve therapeutic antibodies efficacy in cancer patients, several strategies were developed. One of these strategies consists in the enhancement of effector functions. Antibody-dependent cellular cytotoxicity (ADCC) was shown to mediate the activity of several t ...