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Multiple target-based pharmacophore design from active site structures

SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018年第1期29卷 1-19页

作者： Kumar, P. Kaalia, R. Srinivasan, A. Ghosh, I. Jawaharlal Nehru Univ Sch Computat & Integrat Sci New Delhi India Nanyang Technol Univ Biomed Informat Lab Singapore Singapore BITS Dept Comp Sci & Informat Syst Pilani Goa India

Health care systems have benefitted from rational drug discovery processes like vHTS, virtual high throughput screening pharmacophores and quantitative structure-activity relationships, and many challenges have been explored using such techniques: decisions on specificity and selectivity are made after screening millions of molecules for multiple targets. Recent challenges in drug research emphasize the design of drugs that bind with more than one target of interest (multi-target) and do not bind with undesirable targets. this work attempts to use a three-dimensional interaction profile of the active site of a class of proteins, identify selective positions for the binding of functional groups, called features, and develop ensembles of multi-targeted pharmacophores that retain specificity and selectivity. the goal of this study is to develop multi-target pharmacophores by computational methods using protein structures alone to guide the discovery of novel inhibitors of plasmepsins, displaying selectivity over their human homologs, cathepsin D and pepsin. the development of such novel tools is attempted using a combination of different approaches such as the molecular interaction field, clique graph and inductive logic programming to identify and compare specific and selective complementary features. the identification of selective combinations of features has resulted in the design of multi-featured specific and selective pharmacophores that are validated using antimalarial compounds in ChEMBL that are known for their anti-plasmepsin II activity. this novel method is computationally less intensive and is applicable to any known class of target structures for finding specific and selective binders simultaneously.

关键词： Ab initio drug design pharmacophore MIF clique receptor ILP

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Fault-tolerant Quantum Implementation of 1-bit and 4-bit Comparator Circuit using Clifford+T-group

Fault-tolerant Quantum Implementation of 1-bit and 4-bit Com...

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international symposium on Electronic System Design (ISED)

作者： Laxmidhar Biswal Chandan Bandyopadhay Hafizur Rahaman School of VLSI Technology IIEST Shibpur IIEST Shibpur

ISBN: (数字)9781728141770

ISBN: (纸本)9781728141787

Aiming to design a complete Quantum Information Processor (QIP), in this work, we are showing an efficient implementation of fault tolerant quantum comparator circuit. To ensure this fault tolerant property in the design, we have used Clifford+ T-group and also have executed circuit optimization algorithm to contain the cost metrics. In the design phase, initially an optimal 1-bit circuit is formulated and then by integrating 1-bit modules, 4-bit comparator is prepared. though we have shown only 1-bit and 4-bit circuits but it can be generalized for n-bit design as well. Our proposed design is quite different from existing fault-tolerant comparator models as our circuit is magnitude driven design and can compare magnitude of numbers by encoding the input vector into equivalent binary numbers as well. Towards ensuring improved features in our proposed model, the design is transformed to minimum T - depth based design, which in turn ensures minimum CPU cycles to obtain the first output from the design as well reduces the effect of decoherence. In addition to this, the proposed model has optimal T - count metric to control the circuit overhead. the functional correctness of our design also has been checked using several test patterns.

关键词： logic gates Fault tolerance Fault tolerant systems Quantum computing Mathematical model

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Eliminating Irrelevant Non-determinism in functional logic Programs 19th

Eliminating Irrelevant Non-determinism in Functional Logic P...

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19th international symposium on Practical Aspects of Declarative Languages (PADL)

作者： Antoy, Sergio Hanus, Michael Portland State Univ Comp Sci Dept Portland OR 97207 USA CAU Kiel Inst Informat D-24098 Kiel Germany

ISBN: (纸本)9783319516769;9783319516752

functional logic programming languages support nondeterministic search and a flexible use of defined operations by applying them to unknown values. the use of these features has the risk that equal values might be computed several times or I/O computations could fail due to non-deterministic subcomputations. To detect such problems at compile time, we present a method to locate non-deterministic operations. If the non-determinism caused by some operation is semantically not relevant, the programmer can direct the compiler to produce only one result of a computation. If all the results of the computations are equal, this directive preserves the semantics and improves the operational behavior of programs. We define the declarative meaning of such annotations and propose both testing and verification techniques that respectively increase the confidence or formally prove that the non-determinism of an operation is irrelevant.

关键词： Semantics

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functional Reactive programming, Refactored 9

Functional Reactive Programming, Refactored

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9th ACM SIGPLAN symposium on Haskell (Haskell 2016)

作者： Perez, Ivan Baerenz, Manuel Nilsson, Henrik Univ Nottingham Nottingham England Univ Bamberg Bamberg Germany

ISBN: (纸本)9781450344340

functional Reactive programming (FRP) has come to mean many things. Yet, scratch the surface of the multitude of realisations, and there is great commonality between them. this paper investigates this commonality, turning it into a mathematically coherent and practical FRP realisation that allows us to express the functionality of many existing FRP systems and beyond by providing a minimal FRP core parameterised on a monad. We give proofs for our theoretical claims and we have verified the practical side by bench-marking a set of existing, non-trivial Yampa applications running on top of our new system with very good results.

关键词： functional reactive programming reactive programming stream programming monadic streams Haskell

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A Report on the Ninth international Web Rule symposium

A Report on the Ninth International Web Rule Symposium

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9th international symposium on Web Rule Markup and Modeling Initiative (RuleML)

作者： Paschke, Adrian Corp Semant Web AG CSW Berlin Germany FUB Inst Comp Sci Dept Math & Comp Sci Berlin Germany Fraunhofer FOKUS Data Analyt Ctr DANA Berlin Germany RuleML Inc Toronto ON Canada

the annual international Web Rule symposium (RuleML) is an international conferenee on research, applications, languages, and standards for rule technologies. RuleML is a leading conference to build bridges between academe and industry in the field of rules and its applications, especially as part of the semantic technology stack. It is devoted to rule-based programming and rule based systems including production rules systems, logic programming rule engines, and business rule engines/business rule management systems;semantic web rule languages and rule standards;rule-based event-processing languages (EPLs) and technologies;and research on inference rules, transformation rules, decision rules, production rules, and ECA rules. the Ninth international Web Rule symposium (RuleML 2015) was held in Berlin, Germany, August 2-5. this report summarizes the events of that conference.

关键词： logic programming

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Lazy Graph Processing in Haskell 9

Lazy Graph Processing in Haskell

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9th ACM SIGPLAN symposium on Haskell (Haskell 2016)

作者： Dexter, Philip Liu, Yu David Chiu, Kenneth SUNY Binghamton Dept Comp Sci Binghamton NY 13902 USA

ISBN: (纸本)9781450344340

this paper presents a Haskell library for graph processing: DELTA-GRAPH. One unique feature of this system is that intentions to perform graph updates can be memoized in-graph in a decentralized fashion, and the propagation of these intentions within the graph can be decoupled from the realization of the updates. As a result, DELTAGRAPH can respond to updates in constant time and work elegantly with parallelism support. We build a Twitter-like application on top of DELTAGRAPH to demonstrate its effectiveness and explore parallelism and opportunistic computing optimizations.

关键词： functional Data Structures Graph programming

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Haskell 2016 - Proceedings of the 9th international symposium on Haskell, co-located with ICFP 2016

Haskell 2016 - Proceedings of the 9th International Symposiu...

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9th international symposium on Haskell, Haskell 2016, co-located with ICFP 2016

ISBN: (纸本)9781450344340

the proceedings contain 18 papers. the topics discussed include: Revisiting software transactional memory in Haskell;QuickFuzz: an automatic random fuzzer for common file formats;causal commutative arrows revisited;functional reactive programming, refactored;how to twist pointers without breaking them;high-performance client-side web applications through Haskell EDSLs;desugaring Haskell’s do-notation into applicative operations;revisiting software transactional memory in Haskell;autobahn: using genetic algorithms to infer strictness annotations;experience report: types for a relational algebra library;embedding session types in Haskell;and the key monad: type-safe unconstrained dynamic typing.

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High-Performance Client-Side Web Applications through Haskell EDSLs 9

High-Performance Client-Side Web Applications through Haskel...

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9th ACM SIGPLAN symposium on Haskell (Haskell 2016)

作者： Ekblad, Anton Chalmers Univ Technol Gothenburg Sweden

ISBN: (纸本)9781450344340

We present Aplite, a domain-specific language embedded in Haskell for implementing performance-critical functions in client-side web applications. In Aplite, we apply partial evaluation, multi-stage programming and techniques adapted from machine code-targeting, high-performance EDSLs to the domain of web applications. We use Aplite to implement, among other benchmarks, procedural animation using Perlin noise (Perlin 2002), symmetrical encryption and K-means clustering, showing Aplite to be consistently faster than equivalent hand-written JavaScript - up to an order of magnitude for some benchmarks. We also demonstrate how Aplite's multi-staged nature can be used to automatically tune programs to the environment in which they are running, as well as to inputs representative of the programs' intended workload. High-performance computation in the web browser is an attractive goal for many reasons: interactive simulations and games, cryptographic applications and reducing web companies' electricity bills by outsourcing expensive computations to users' web browsers. Similarly, functional programming in the browser is attractive due to its promises of simpler, shorter, safer programs. In this paper, we propose a way to combine the two.

关键词： domain-specific languages web applications multi-stage programming

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Supermonads One Notion to Bind them All 9

Supermonads One Notion to Bind Them All

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9th ACM SIGPLAN symposium on Haskell (Haskell 2016)

作者： Bracker, Jan Nilsson, Henrik Univ Nottingham Sch Comp Sci Funct Programming Lab Nottingham England

ISBN: (纸本)9781450344340

Several popular generalizations of monads have been implemented in Haskell. Unfortunately, because the shape of the associated type constructors do not match the standard Haskell monad interface, each such implementation provides its own type class and versions of associated library functions. Furthermore, simultaneous use of different monadic notions can be cumbersome as it in general is necessary to be explicit about which notion is used where. In this paper we introduce supermonads: an encoding of monadic notions that captures several different generalizations along with a version of the standard library of monadic functions that work uniformly with all of them. As standard Haskell type inference does not work for supermonads due to their generality, our supermonad implementation is accompanied with a language extension, in the form of a plugin for the Glasgow Haskell Compiler (GHC), that allows type inference for supermonads, obviating the need for manual annotations.

关键词： functional programming Glasgow Haskell Compiler Haskell monads syntactic support type checker plugin

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the Key Monad: Type-Safe Unconstrained Dynamic Typing 9

The Key Monad: Type-Safe Unconstrained Dynamic Typing

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9th ACM SIGPLAN symposium on Haskell (Haskell 2016)

作者： van der Ploeg, Atze Claessen, Koen Buiras, Pablo Chalmers Univ Technol Gothenburg Sweden Harvard Univ Cambridge MA 02138 USA

ISBN: (纸本)9781450344340

We present a small extension to Haskell called the Key monad. With the Key monad, unique keys of different types can be created and can be tested for equality. When two keys are equal, we also obtain a concrete proof that their types are equal. this gives us a form of dynamic typing, without the need for Typeable constraints. We show that our extension allows us to safely do things we could not otherwise do: it allows us to implement the ST monad (inefficiently), to implement an embedded form of arrow notation, and to translate parametric HOAS to typed de Bruijn indices, among others. Although strongly related to the ST monad, the Key monad is simpler and might be easier to prove safe. We do not provide such a proof of the safety of the Key monad, but we note that, surprisingly, a full proof of the safety of the ST monad also remains elusive to this day. Hence, another reason for studying the Key monad is that a safety proof for it might be a stepping stone towards a safety proof of the ST monad.

关键词： functional programming Haskell Higher-order state ST monad Arrow notation Parametric HOAS

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