These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
166 related articles for article (PubMed ID: 11854494)
21. Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. He Y; Xiao Y; Liwo A; Scheraga HA J Comput Chem; 2009 Oct; 30(13):2127-35. PubMed ID: 19242966 [TBL] [Abstract][Full Text] [Related]
22. A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes. Stumpff-Kane AW; Feig M Proteins; 2006 Apr; 63(1):155-64. PubMed ID: 16397892 [TBL] [Abstract][Full Text] [Related]
23. Design of a knowledge-based force field for off-lattice simulations of protein structure. Liwo A; Ołdziej S; Kaźmierkiewicz R; Groth M; Czaplewski C Acta Biochim Pol; 1997; 44(3):527-47. PubMed ID: 9511963 [TBL] [Abstract][Full Text] [Related]
24. Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling. Wang C; Wei Y; Zhang H; Kong L; Sun S; Zheng WM; Bu D BMC Bioinformatics; 2019 Mar; 20(Suppl 3):135. PubMed ID: 30925867 [TBL] [Abstract][Full Text] [Related]
25. A free-energy approach for all-atom protein simulation. Verma A; Wenzel W Biophys J; 2009 May; 96(9):3483-94. PubMed ID: 19413955 [TBL] [Abstract][Full Text] [Related]
26. Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide. Cavalli A; Vendruscolo M; Paci E Biophys J; 2005 May; 88(5):3158-66. PubMed ID: 15749768 [TBL] [Abstract][Full Text] [Related]
27. Conformational Sampling of a Biomolecular Rugged Energy Landscape. Rydzewski J; Jakubowski R; Nicosia G; Nowak W IEEE/ACM Trans Comput Biol Bioinform; 2018; 15(3):732-739. PubMed ID: 27913358 [TBL] [Abstract][Full Text] [Related]
28. Exploration of the conformational space of oxytocin and arginine-vasopressin using the electrostatically driven Monte Carlo and molecular dynamics methods. Liwo A; Tempczyk A; Ołdziej S; Shenderovich MD; Hruby VJ; Talluri S; Ciarkowski J; Kasprzykowski F; Lankiewicz L; Grzonka Z Biopolymers; 1996 Feb; 38(2):157-75. PubMed ID: 8589250 [TBL] [Abstract][Full Text] [Related]
29. Energy landscapes for proteins described by the UNRES coarse-grained potential. Wesołowski PA; Sieradzan AK; Winnicki MJ; Morgan JWR; Wales DJ Biophys Chem; 2023 Dec; 303():107107. PubMed ID: 37862761 [TBL] [Abstract][Full Text] [Related]
30. Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures. Vila JA; Ripoll DR; Scheraga HA Proc Natl Acad Sci U S A; 2003 Dec; 100(25):14812-6. PubMed ID: 14638943 [TBL] [Abstract][Full Text] [Related]
31. The protein folding problem: global optimization of the force fields. Scheraga HA; Liwo A; Oldziej S; Czaplewski C; Pillardy J; Ripoll DR; Vila JA; Kazmierkiewicz R; Saunders JA; Arnautova YA; Jagielska A; Chinchio M; Nanias M Front Biosci; 2004 Sep; 9():3296-323. PubMed ID: 15353359 [TBL] [Abstract][Full Text] [Related]
32. Calculation of protein conformation by global optimization of a potential energy function. Lee J; Liwo A; Ripoll DR; Pillardy J; Scheraga HA Proteins; 1999; Suppl 3():204-8. PubMed ID: 10526370 [TBL] [Abstract][Full Text] [Related]
33. Energetics of the native and non-native states of the glycophorin transmembrane helix dimer. Mottamal M; Zhang J; Lazaridis T Proteins; 2006 Mar; 62(4):996-1009. PubMed ID: 16395713 [TBL] [Abstract][Full Text] [Related]
34. Determination of the conformation of folding initiation sites in proteins by computer simulation. Avbelj F; Moult J Proteins; 1995 Oct; 23(2):129-41. PubMed ID: 8592695 [TBL] [Abstract][Full Text] [Related]
35. A stochastic algorithm for global optimization and for best populations: a test case of side chains in proteins. Glick M; Rayan A; Goldblum A Proc Natl Acad Sci U S A; 2002 Jan; 99(2):703-8. PubMed ID: 11792838 [TBL] [Abstract][Full Text] [Related]
36. Addition of side chains to a known backbone with defined side-chain centroids. Kaźmierkiewicz R; Liwo A; Scheraga HA Biophys Chem; 2003; 100(1-3):261-80. PubMed ID: 12646370 [TBL] [Abstract][Full Text] [Related]
37. Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions. Zacharias M; Sklenar H Biophys J; 1997 Dec; 73(6):2990-3003. PubMed ID: 9414214 [TBL] [Abstract][Full Text] [Related]
38. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Schueler-Furman O; Wang C; Baker D Proteins; 2005 Aug; 60(2):187-94. PubMed ID: 15981249 [TBL] [Abstract][Full Text] [Related]
39. How well can we predict native contacts in proteins based on decoy structures and their energies? Zhu J; Zhu Q; Shi Y; Liu H Proteins; 2003 Sep; 52(4):598-608. PubMed ID: 12910459 [TBL] [Abstract][Full Text] [Related]
40. Noncontact dipole effects on channel permeation. II. Trp conformations and dipole potentials in gramicidin A. Dorigo AE; Anderson DG; Busath DD Biophys J; 1999 Apr; 76(4):1897-908. PubMed ID: 10096887 [TBL] [Abstract][Full Text] [Related] [Previous] [Next] [New Search]