FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2024552181> ?p ?o ?g. }

• W2024552181 endingPage "1250" @default.
• W2024552181 startingPage "1241" @default.
• W2024552181 abstract "Predicting protein-protein and protein-ligand docking remains one of the challenging topics of structural biology. The main problems are (i) to reliably estimate the binding free energies of docked states, (ii) to enumerate possible docking orientations at a high resolution, and (iii) to consider mobility of the docking surfaces and structural rearrangements upon interaction. Here we present a novel algorithm, TreeDock, that addresses the enumeration problem in a rigid-body docking search. By representing molecules as multidimensional binary search trees and by exploring a sufficient number of docking orientations such that two chosen atoms, one from each molecule, are always in contact, TreeDock is able to explore all clash-free orientations at very fine resolution in a reasonable amount of time. Due to the speed of the program, many contact pairs can be examined to search partial or complete surface areas. The deterministic systematic search of TreeDock is in contrast to most other docking programs that use stochastic searches such as Monte Carlo or simulated annealing methods. At this point, we have used the Lennard-Jones potential as the only scoring function and show that this can predict the correct docked conformation for a number of protein-protein and protein-ligand complexes. The program is most powerful if some information is known about the location of binding faces from NMR chemical-shift perturbation studies, orientation information from residual dipolar coupling, or mutational screening. The approach has the potential to include docking-site mobility by performing molecular dynamics or other randomization methods of the docking site and docking families to families of structures. The performance of the algorithm is demonstrated by docking three complexes of immunoglobulin superfamily domains, CD2 to CD58, the V(alpha) domain of a T-cell receptor to its V(beta) domain, and a T-cell receptor to a pMHC complex as well as a small molecule inhibitor to a phosphatase." @default.
• W2024552181 created "2016-06-24" @default.
• W2024552181 creator A5020247340 @default.
• W2024552181 creator A5090569228 @default.
• W2024552181 date "2002-01-25" @default.
• W2024552181 modified "2023-10-14" @default.
• W2024552181 title "TreeDock: A Tool for Protein Docking Based on Minimizing van der Waals Energies" @default.
• W2024552181 cites W1563020763 @default.
• W2024552181 cites W1787469221 @default.
• W2024552181 cites W1970119605 @default.
• W2024552181 cites W1972091733 @default.
• W2024552181 cites W1979453000 @default.
• W2024552181 cites W1979670056 @default.
• W2024552181 cites W1982176049 @default.
• W2024552181 cites W1995017064 @default.
• W2024552181 cites W2000383223 @default.
• W2024552181 cites W2015290017 @default.
• W2024552181 cites W2023940675 @default.
• W2024552181 cites W2035273655 @default.
• W2024552181 cites W2050654179 @default.
• W2024552181 cites W2055577518 @default.
• W2024552181 cites W2064514012 @default.
• W2024552181 cites W2067323612 @default.
• W2024552181 cites W2067455153 @default.
• W2024552181 cites W2067872997 @default.
• W2024552181 cites W2080653934 @default.
• W2024552181 cites W2090078310 @default.
• W2024552181 cites W2138031164 @default.
• W2024552181 cites W2155292823 @default.
• W2024552181 cites W2158534713 @default.
• W2024552181 cites W2165558283 @default.
• W2024552181 cites W2170820778 @default.
• W2024552181 cites W2911302472 @default.
• W2024552181 doi "https://doi.org/10.1021/ja011240x" @default.
• W2024552181 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/11841293" @default.
• W2024552181 hasPublicationYear "2002" @default.
• W2024552181 type Work @default.
• W2024552181 sameAs 2024552181 @default.
• W2024552181 citedByCount "62" @default.
• W2024552181 countsByYear W20245521812012 @default.
• W2024552181 countsByYear W20245521812013 @default.
• W2024552181 countsByYear W20245521812014 @default.
• W2024552181 countsByYear W20245521812017 @default.
• W2024552181 countsByYear W20245521812018 @default.
• W2024552181 countsByYear W20245521812019 @default.
• W2024552181 countsByYear W20245521812021 @default.
• W2024552181 countsByYear W20245521812022 @default.
• W2024552181 crossrefType "journal-article" @default.
• W2024552181 hasAuthorship W2024552181A5020247340 @default.
• W2024552181 hasAuthorship W2024552181A5090569228 @default.
• W2024552181 hasConcept C103697762 @default.
• W2024552181 hasConcept C105795698 @default.
• W2024552181 hasConcept C11413529 @default.
• W2024552181 hasConcept C116887118 @default.
• W2024552181 hasConcept C119145174 @default.
• W2024552181 hasConcept C126061179 @default.
• W2024552181 hasConcept C126980161 @default.
• W2024552181 hasConcept C147597530 @default.
• W2024552181 hasConcept C159110408 @default.
• W2024552181 hasConcept C178790620 @default.
• W2024552181 hasConcept C185592680 @default.
• W2024552181 hasConcept C19499675 @default.
• W2024552181 hasConcept C32909587 @default.
• W2024552181 hasConcept C33923547 @default.
• W2024552181 hasConcept C41008148 @default.
• W2024552181 hasConcept C41685203 @default.
• W2024552181 hasConcept C44695244 @default.
• W2024552181 hasConcept C47701112 @default.
• W2024552181 hasConcept C55493867 @default.
• W2024552181 hasConcept C59593255 @default.
• W2024552181 hasConcept C71924100 @default.
• W2024552181 hasConcept C77319485 @default.
• W2024552181 hasConceptScore W2024552181C103697762 @default.
• W2024552181 hasConceptScore W2024552181C105795698 @default.
• W2024552181 hasConceptScore W2024552181C11413529 @default.
• W2024552181 hasConceptScore W2024552181C116887118 @default.
• W2024552181 hasConceptScore W2024552181C119145174 @default.
• W2024552181 hasConceptScore W2024552181C126061179 @default.
• W2024552181 hasConceptScore W2024552181C126980161 @default.
• W2024552181 hasConceptScore W2024552181C147597530 @default.
• W2024552181 hasConceptScore W2024552181C159110408 @default.
• W2024552181 hasConceptScore W2024552181C178790620 @default.
• W2024552181 hasConceptScore W2024552181C185592680 @default.
• W2024552181 hasConceptScore W2024552181C19499675 @default.
• W2024552181 hasConceptScore W2024552181C32909587 @default.
• W2024552181 hasConceptScore W2024552181C33923547 @default.
• W2024552181 hasConceptScore W2024552181C41008148 @default.
• W2024552181 hasConceptScore W2024552181C41685203 @default.
• W2024552181 hasConceptScore W2024552181C44695244 @default.
• W2024552181 hasConceptScore W2024552181C47701112 @default.
• W2024552181 hasConceptScore W2024552181C55493867 @default.
• W2024552181 hasConceptScore W2024552181C59593255 @default.
• W2024552181 hasConceptScore W2024552181C71924100 @default.
• W2024552181 hasConceptScore W2024552181C77319485 @default.
• W2024552181 hasIssue "7" @default.
• W2024552181 hasLocation W20245521811 @default.
• W2024552181 hasLocation W20245521812 @default.
• W2024552181 hasOpenAccess W2024552181 @default.

• next