A new molecular simulation software package – Peking University Drug Design System (PKUDDS) for structure-based drug design

Hou, Tingjun; Xu, Xiaowei

doi:10.1016/s1093-3263(00)00094-2

Cited by 8 publications

(4 citation statements)

References 18 publications

(18 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There are several screening methods in modern computer-aided drug design. For example, molecular docking can be used to study the interaction between bioactive ingredient and target enzyme when the target 3-D structure is known. − Pharmacophore searching can be used to search candidate compounds with specific pharmacophoric groups. Further, candidate compounds may be extracted from respective herbs and be subjected to bioactivity and toxicity test.…”

Section: Discussionmentioning

confidence: 99%

A 3D Structure Database of Components from Chinese Traditional Medicinal Herbs

Qiao

Hou

Wei

et al. 2002

J. Chem. Inf. Comput. Sci.

Self Cite

View full text Add to dashboard Cite

This article described a 3D structure database of components extracted from Chinese Traditional Medicinal (CTM) herbs. It offers not only basic molecular properties and optimized 3D structure of the compounds but also detailed information on their herbal origin, including basic herbal category (e.g. English name, Latin name, and family), effective parts, and clinical effects. An easy to use, interactive GUI browser allows users to perform various searches via complex logical query builder. Combined with the latest network database engine (MySQL), it can achieve excellent performance under both a local network and an Internet environment. We have tested it on the design of inhibitors of NS3-NS4A protease. Results show that the structure database of components extracted from Chinese medicinal herbs can be a rich source in searching the lead compound.

show abstract

Section: Discussionmentioning

confidence: 99%

A 3D Structure Database of Components from Chinese Traditional Medicinal Herbs

Qiao

Hou

Wei

et al. 2002

J. Chem. Inf. Comput. Sci.

Self Cite

View full text Add to dashboard Cite

show abstract

“…GAs have also been advocated for drug design though, surprisingly, only a few papers have been published in this area, including their use in tools for drug design (Hou and Xu 2001) and some review papers Terfloth and Gasteiger 2001).…”

Section: Gas and Designmentioning

confidence: 99%

AI and OR in management of operations: history and trends

Kobbacy

Vadera

Rasmy

2007

Journal of the Operational Research Society

View full text Add to dashboard Cite

The last decade has seen a considerable growth in the use of AI for operations management with the aim of finding solutions to problems that are increasing in complexity and scale. This paper begins by setting the context for the survey through a historical perspective of OR and AI. An extensive survey of applications of AI techniques for operations management, covering a total of over 1200 papers published from 1995 to 2004 is then presented. The papers are categorised into four areas of operations management: (a) design, (b) scheduling, (c) process planning and control and (d) quality, maintenance and fault diagnosis. Each of the four areas is categorised in terms of the AI techniques used: genetic algorithms, case based reasoning, knowledge based systems, fuzzy logic and hybrid techniques. The trends over the last decade are identified, discussed with respect to expected trends and directions for future work suggested.

show abstract

“…Multifunctional Web-based design tools , have been developed to facilitate protein design. The most popular protein design tool is Rosetta, a software suite based on the MC technique. − The Rosetta program exhibits broad applicability for predicting and designing the components, structures, and functionalities of proteins.…”

Section: Introductionmentioning

confidence: 99%

Designing Peptide Sequences in Flexible Chain Conformations to Bind RNA: A Search Algorithm Combining Monte Carlo, Self-Consistent Mean Field and Concerted Rotation Techniques

Xiao

Agris

Hall

2015

J. Chem. Theory Comput.

View full text Add to dashboard Cite

A search algorithm combining Monte Carlo, self-consistent mean field, and concerted rotation techniques was developed to discover peptide sequences that are reasonable HIV drug candidates due to their exceptional binding to human tRNAUUU(Lys3), the primer of HIV replication. The search algorithm allows for iteration between sequence mutations and conformation changes during sequence evolution. Searches conducted for different classes of peptides identified several potential peptide candidates. Analysis of the energy revealed that the asparagine and cysteine at residues 11 and 12 play important roles in "recognizing" tRNA(Lys3) via van der Waals interactions, contributing to binding specificity. Arginines preferentially attract the phosphate linkage via charge-charge interaction, contributing to binding affinity. Evaluation of the RNA/peptide complex's structure revealed that adding conformation changes to the search algorithm yields peptides with better binding affinity and specificity to tRNA(Lys3) than a previous mutation-only algorithm.

show abstract

A new molecular simulation software package – Peking University Drug Design System (PKUDDS) for structure-based drug design

Cited by 8 publications

References 18 publications

A 3D Structure Database of Components from Chinese Traditional Medicinal Herbs

A 3D Structure Database of Components from Chinese Traditional Medicinal Herbs

AI and OR in management of operations: history and trends

Designing Peptide Sequences in Flexible Chain Conformations to Bind RNA: A Search Algorithm Combining Monte Carlo, Self-Consistent Mean Field and Concerted Rotation Techniques

Contact Info

Product

Resources

About