Generation of crystal structures using known crystal structures as analogues

Cole, Jason C.; Groom, Colin R.; Read, Murray G.; Giangreco, Ilenia; McCabe, Patrick; Reilly, Anthony M.; Shields, Gregory P.

doi:10.1107/s2052520616006533

Cited by 19 publications

(12 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Deep learning approaches, which most commonly rely on many-layered ANNs or a combination of ANNs with other learning techniques such as Boltzmann machines, are showing particular promise for predicting chemical synthesis routes by combining rulesbased expert systems with neural networks that rank the candidates, 36 or rank the likelihood of a predicted product by applying the rules. 37 One ANN that learned from chemical literature examples was able to achieve a level of sophistication such that trained chemists could not distinguish between computer and human expert designed routes. 34 However, a severe drawback of rules-based systems is that they have difficulty operating outside their knowledge base.…”

Section: Guiding Chemical Synthesismentioning

confidence: 99%

Machine learning for molecular and materials science

Butler

Davies

Cartwright

et al. 2018

Nature

3,028

2,126

View full text Add to dashboard Cite

show abstract

Section: Guiding Chemical Synthesismentioning

confidence: 99%

Machine learning for molecular and materials science

Butler

Davies

Cartwright

et al. 2018

Nature

3,028

2,126

View full text Add to dashboard Cite

show abstract

“…16 Disorder plays a different role in different types of materials, but it is notable that one prediction made at the CCDC's 50 th party 17 was that in another 50 years, all organic crystal structures would be disordered. Does using data on known crystal structures (such as the Cambridge Structural Database) 18,19 risk bias from sociological inuences on research and reporting or historic limitations in analytical capabilities?…”

Section: Search Coverage In Csp_0 Structure Generationmentioning

confidence: 99%

Is zeroth order crystal structure prediction (CSP_0) coming to maturity? What should we aim for in an ideal crystal structure prediction code?

Price

2018

Faraday Discuss.

117

View full text Add to dashboard Cite

Crystal structure prediction based on searching for the global minimum in the lattice energy (CSP_0) is growing in use for guiding the discovery of new materials, for example, new functional materials, new phases of interest to planetary scientists and new polymorphs relevant to pharmaceutical development. This Faraday Discussion can assess the progress of CSP_0 over the range of types of materials to which CSP is currently and could be applied, which depends on our ability to model the variety of interatomic forces in crystals. The basic hypothesis, that the outcome of crystallisation is determined by thermodynamics, needs examining by considering methods of modelling relative thermodynamic stability not only as a function of pressure and temperature, but also of size, solvent and the presence of heterogeneous templates or impurities (CSP_thd). Given that many important materials persist, and indeed may be formed, when they are not the most thermodynamically stable structure, we need to define what would be required of an ideal CSP code (CSP_aim).

show abstract

“…Desolvation energy is a prime parameter that decides a molecules interaction with its pharmacodynamic target [5]. In the biological environment, all drug binding pockets of a target protein remain solvated, and hence, a ligand cannot as such occupy the active site unless it dislodges the water molecules.…”

Section: Discussionmentioning

confidence: 99%

“…FASTA sequence of the retrieved structure revealed the presence of glycine at position. The target was preprocessed by standard methods before binding analysis [5].…”

Section: Retrieval Of Crystal Structure and Target Preparationmentioning

confidence: 99%

In Silico and in Vivo Pharmacological Studies of Clozapine and D-Amino Acid Oxidase Inhibitor for Cognitive Enhancement

Nithya

Shanmugarajan

2018

Asian J Pharm Clin Res

View full text Add to dashboard Cite

Objective: D-amino acid oxidase inhibitors (DAAOIs) are of particular focus for cognition study. Atypical antipsychotics are known DAAO inhibitors. The present examination was done to check out the binding affinity of atypical antipsychotics by docking toward the DAAO protein; in conclusion, the picked antipsychotic drug was checked for their cognition enhancing activity with scopolamine-induced amnesia.Methods: The crystal structure of DAAO was obtained from Protein Data Bank, the energy minimization was performed with CHARMM program, then active site prediction was made out using Ramachandran plot, and finally, docking examination was finished using Autodock 4.2 tool. For in vivo study, the mice were divided into three groups. Group I - vehicle (Saline) treated, Group II – saline +scopolamine (1 mg/kg, intraperitoneal [i.p]) treated, and Group III - clozapine (20 mg/kg, i.p) + scopolamine (1 mg/kg, i.p).Results: The Autodock examination shows significant binding affinity of - 5.22 for brexpiprazole and least or positive binding affinity of +1 for iloperidone. Clozapine with binding energy of - 2.87 was decided for completing the in vivo cognition study. The in vivo shows up that clozapine (20 mg/kg, i.p) exhibits a change in the impairment of spatial memory.Conclusion: The results recommend that the clozapine produces cognitive enhancement through both DAAOI and antipsychotic action. Clozapine has cognitive improvement potential, favoring its usage in reducing toxic impacts of scopolamine

show abstract

Generation of crystal structures using known crystal structures as analogues

Abstract: An investigation into using shape-similarity of molecules to generate putative crystal structures.

Cited by 19 publications

References 76 publications

Machine learning for molecular and materials science

Machine learning for molecular and materials science

Is zeroth order crystal structure prediction (CSP_0) coming to maturity? What should we aim for in an ideal crystal structure prediction code?

In Silico and in Vivo Pharmacological Studies of Clozapine and D-Amino Acid Oxidase Inhibitor for Cognitive Enhancement

Contact Info

Product

Resources

About