Paulina Mata

SPROUT: a program for structure generation.

SummarySPROUT is a new computer program for constrained structure generation that is designed to generate molecules for a range of applications in molecular recognition. It uses artificial intelligence techniques to moderate the combinatorial explosion that is inherent in structure generation. The program is presented here for the design of enzyme inhibitors. Structure generation is divided into two phases: (i) primary structure generation to produce molecular graphs to fit the steric constraints; and (ii) secondary structure generation which is the process of introducing appropriate functionality to the graphs to produce molecules that satisfy the secondary constraints, e.g., electrostatics and hydrophobicity. Primary structure generation has been tested on two enzyme receptor sites; the p-amidino-phenyl-pyruvate binding site of trypsin and the acetyl pepstatin binding site of HIV-1 protease. The program successfully generates structures that resemble known substrates and, more importantly, the predictive power of the program has been demonstrated by its ability to suggest novel structures.

SPROUT: recent developments in the de novo design of molecules.

SPROUT is a computer program for constrained structure generation. It is designed to generate molecules for a range of applications in molecular recognition. The program uses a number of approximations that enable a wide variety of diverse structures to be generated. Practical use of the program is demonstrated in two examples. The first demonstrates the ability of the program to generate candidate inhibitors for a receptor site of known 3D structure, specifically the GDP binding site of p21. In the second example, structures are generated to fit a pharmacophore hypothesis that models morphine agonists.

The CIP sequence rules: Analysis and proposal for a revision

Abstract In spite of their value and wide usage the Cahn, Ingold and Prelog (CIP) Sequence Rules have some deficiencies. In particular incompleteness, inconsistency and ambiguity can arise in their application to complex molecules. Therefore, a complete analysis of the CIP Sequence Rules has been made and modified rules are proposed.

Implementation of the Cahn-Ingold-Prelog System for Stereochemical Perception in the LHASA Program

The CIP system for identification and specification of stereogenic units has been implemented in the LHASA program. This new implementation of the CIP system, according to its 1982 revision, is described. The main improvements introduced are an extension of the capabilities for handling the representations of stereobonds, for the identification of stereogenic centers (chiral and pseudoasymmetric), prochiral centers, and double bonds, and mainly in the implementation of the CIP sequence rules for comparison of the ligands.

Optimisation of gellan gum edible coating for ready-to-eat mango (Mangifera indica L.) bars

The optimisation of an edible coating based on low acyl (L)/high acyl (H) gellan gum for ready-to-eat mango bars was performed through a central composite rotatable design (CCRD). The independent variables were the concentration of gellan (L/H90/10) and the concentration of Ca(2+) in the coating solution, as well as the storage time after coating application. The response variables studied were the coating thickness, mango bars firmness, syneresis, and colour alterations. Gellan concentration was the independent variable that most influenced the thickness of the coating. Syneresis was quite low for the conditions tested (<1.64%). Similarly, the colour alterations were low during the entire storage time (ΔE<5). Considering the model predictions, 1.0%wt L/H90/10 with addition of 6 mM Ca(2+) could represent the optimal coating formulation for the mango bars. The release of eight volatile compounds from the uncoated and coated mango bars with the selected formulation was analysed by Headspace - Solid Phase Micro Extraction-Gas Chromatography during 9 days of refrigerated storage. This work showed that the coating can improve mango bars sensory characteristics (appearance and firmness) and stability in terms of syneresis, colour and volatiles content during storage increasing the commercial value of the final product.

COMPARISON OF CONSTITUTIONAL PROPERTIES IN THE CIP SYSTEM: THE CIP SEQUENCE RULE 1

Abstract An analysis of the CIP Sequence Rules was recently published in this journal 1 . However, further work on the implementation of the CIP Rules for computer use suggested that a reformulation of Sequence Rule 1 was required. In this paper this Rule is analyzed and its modification proposed.

The CIP System Again: Respecting Hierarchies Is Always a Must

In a recent paper published in this journal, a computational implementation of the Cahn−Ingold−Prelog (CIP) rules was reported and a new subrule was proposed to rank complex ligands containing chiral centers. In this paper, it is demonstrated that this new subrule is unnecessary and its need only results from an oversimplified implementation of the CIP system.

Comment on "Response to the comment on exhaustive generation of organic isomers. 5. Unsaturated optical and geometrical stereoisomers and a new CIP subrule"

to the Brecher comment 3 was published. In this answer, 4 the authors recognize that their subrule was not necessary to rank the ligands they originally provided to justify it; however they insist on the need for the subrule in other situations. They also state that the new criterion should be applied one step after the CIP rules, and only if analysis according to those rules gives no precedence to any of the ligands being compared.