The past decade has brought major advances in the quality and variety of methods for computerized drug design and molecular docking, making the area ripe for the implementation of hybrid algorithms. Hybrid methods create improved algorithms from existing ones by mixing techniques in a way that maximizes advantages and minimizes disadvantages. Here, we outline a hybrid method for molecular docki...

Lead Optimisation is the process by which a chemical lead series is improved with regard to multiple properties. These properties will vary from project to project but typically include affinity at the target protein, ADME properties and certain toxicological end-points. Techniques from computational chemistry and cheminformatics have a key role to play in many aspects of lead optimisation. A n...

There is immense pressure on all developers of new drugs today to efficiently and costeffectively produce compounds with efficacies better than existing therapies and with very limited adverse effects. This requires the simultaneous optimization of both the desired bioactivity and the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of a drug candidate. Of the ADM...

Internet technology offers an excellent opportunity for the development of tools by the cooperative effort of various groups and institutions. We have developed a multi-platform software system, Virtual Computational Chemistry Laboratory, http://www.vcclab.org, allowing the computational chemist to perform a comprehensive series of molecular indices/properties calculations and data analysis. Th...

In order to illustrate how atomistic modeling is being used to determine the structure, physical, and chemical properties of materials at the nanoscale, we present here the results of molecular dynamics (MD) simulations on nanoscale assemblies of such materials as carbon nanotubes, diamond surfaces, metal alloy nanowires, and ceramics. We also include here the results of nonequilibrium MD simul...

| Three negative results: 1. Given a set of allowed starting materials and allowed chemical reactions, the problem of determining whether a chemical of speciied structure is synthesizable is Turing undecidable. 2. The question of whether it is synthesizable in N steps is NP-hard. These results apply in a general abstract setting and do not prove anything about how hard the problem is with any s...

This chapter discusses molecular mechanics (MM)-based approaches to investigate organometallic complexes. In particular, ligand field MM (LFMM), “Sum of Interactions Between Fragments Ab Initio” (SIBFA), and VALBOND with its extension to VALBOND-TRANS are presented in some detail. Two particular applications of VALBOND-TRANS to an Ir(III) and a Pt(II) complex are presented. Possible future exte...

Theoretical and Computational Chemistry has seen a remarkable development in the past decades. While it started as a discipline of a few experts in the 1960s, the field has grown enormously due to advances in computational resources and software packages. In addition to the dramatic increase in computer power, a wide range of methods with predictive capabilities such as density functional theor...

Molecular dynamics is a general technique for simulating the time-dependent properties of molecules and their environments. Quantum mechanics, as applied to molecules or clusters of molecules, provides a prescription for predicting properties exactly (in principle). It is reasonable to expect that both will have a profound effect on our understanding of environmental chemistry in the future. In...

The experimental assessment of absorption, distribution, metabolism, excretion, toxicity and related physiochemical properties of small molecules is counted among the most timeand cost-intensive tasks in chemical research. Computational approaches, such as machine learning methods, represent an economic alternative to predict these properties, however, the limited accuracy and irregular error r...