8 research outputs found
Knowledge-based energy functions for computational studies of proteins
- Author
- A. Ben-Naim
- A. Godzik
- A. Godzik
- A. Rossi
- A.J. Bordner
- A.V. Finkelstein
- B. Fain
- B. Krishnamoorthy
- B. Kuhlman
- B. Schölkopf
- B.H. Park
- B.I. Dahiyat
- B.J. McConkey
- B.O. Mitchell
- C. Anfinsen
- C. Carter Jr.
- C. Czaplewski
- C. Hoppe
- C. Hu
- C. Micheletti
- C. Papadimitriou
- C. Zhang
- C. Zhang
- C. Zhang
- C. Zhang
- C. Zhang
- C.A. Rohl
- C.B. Anfinsen
- C.M.R Lemer
- C.S. Mészáros
- D. Gilis
- D. Gilis
- D. Gilis
- D. Tobi
- D. Xu
- E. Venclovas
- E.I. Shakhnovich
- E.I. Shakhnovich
- F.A. Momany
- H. Dobbs
- H. Edelsbrunner
- H. Gan
- H. Li
- H. Li
- H. Lu
- H. Zhou
- H.S. Chan
- I. Muegge
- J. Khatun
- J. Liang
- J.A. Kocher
- J.A. Rank
- J.M. Deutsch
- J.R. Bienkowska
- K. Nishikawa
- K. Sale
- K.H. Lee
- K.K. Koretke
- K.K. Koretke
- K.T. Simons
- L. Adamian
- L. Adamian
- L. Adamian
- L.A. Mirny
- L.L. Looger
- L.M. Amzel
- M. Karplus
- M. Levitt
- M. Vendruscolo
- M. Vendruscolo
- M.H. Hao
- M.H. Hao
- M.J. Sippl
- M.J. Sippl
- M.J. Sippl
- M.P. Eastwood
- M.R. Betancourt
- M.S. Friedrichs
- N. Karmarkar
- N.V. Buchete
- N.V. Buchete
- P. Koehl
- P. Koehl
- P.D. Thomas
- P.D. Thomas
- P.G. Wolynes
- P.J. Munson
- R. Goldstein
- R. Guerois
- R. Jackups Jr.
- R. Janicke
- R. MĂ©ndez
- R. Samudrala
- R. Samudrala
- R.B. Hill
- R.I. Dima
- R.J. Vanderbei
- R.K. Singh
- R.L. Jernigan
- R.S. DeWitte
- S. Liu
- S. Miyazawa
- S. Miyazawa
- S. Miyazawa
- S. Shimizu
- S. Shimizu
- S. Tanaka
- S.J. Wodak
- T. Kortemme
- T. Kortemme
- T. Kortemme
- T. Lazaridis
- T.L. Chiu
- U. Bastolla
- U. Bastolla
- V. Vapnik
- V. Vapnik
- V.N. Maiorov
- W.P. Russ
- X. Li
- X. Li
- Y. Duan
- Y. Park
- Y. Xia
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 19/01/2006
- Field of study
This chapter discusses theoretical framework and methods for developing
knowledge-based potential functions essential for protein structure prediction,
protein-protein interaction, and protein sequence design. We discuss in some
details about the Miyazawa-Jernigan contact statistical potential,
distance-dependent statistical potentials, as well as geometric statistical
potentials. We also describe a geometric model for developing both linear and
non-linear potential functions by optimization. Applications of knowledge-based
potential functions in protein-decoy discrimination, in protein-protein
interactions, and in protein design are then described. Several issues of
knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe
Polarization Measurements in High-Energy Deuteron Photodisintegration
- Author
- A. A. Zybalov
- A. Afanasev
- A. Afanasev
- A. E. L. Dieperink
- A. I. Akhiezer
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. S. Bratashevskij
- A. Saha
- A. Sarty
- B. Bonin
- B. Fox
- B. Wojtsekhowski
- C. Bochna
- C. C. Chang
- C. Carlson
- C. F. Perdrisat
- C. Glashausser
- C. Jones
- C. W. de Jager
- D. Abbott
- D. Crovelli
- D. Dutta
- D. G. Crabb
- D. J. Margaziotis
- D. Meekins
- D. Simon
- E. Brash
- E. C. Schulte
- E. Chudakov
- E. De Sanctis
- E. Kinney
- E. Kooijman
- F. Adamian
- F. F. Liu
- F. Garibaldi
- F. Xiong
- G. Kumbartzki
- G. M. Huber
- G. M. Urciuoli
- H. Gao
- H. Ikeda
- H. Ikeda
- H. Olsen
- H. Tanabe
- J. Calarco
- J. E. Belz
- J. Gao
- J. Gomez
- J. Hovdebo
- J. Kelly
- J. LeRose
- J. M. Laget
- J. Mitchell
- J. Napolitano
- J. P. Chen
- K. Aniol
- K. Benslama
- K. Fissum
- K. McCormick
- K. Wijesooriya
- L. A. Kondratyuk
- L. Bimbot
- L. C. Alexa
- L. L. Frankfurt
- L. L. Frankfurt
- L. Morand
- L. Todor
- M. Amarian
- M. Epstein
- M. K. Jones
- M. K. Jones
- M. Kuss
- M. Liang
- M. Rvachev
- M. Schwamb
- M. W. McNaughton
- N. E. Cheung
- N. Liyanage
- O. Gayou
- O. Hansen
- P. Bosted
- P. E. Ulmer
- P. Markowitz
- R. Arnold
- R. D. Ransome
- R. Gilman
- R. Holt
- R. J. Holt
- R. L. Anderson
- R. Lindgren
- R. Michaels
- R. Pomatsalyuk
- R. Roche
- R. Suleiman
- S. Becher
- S. Choi
- S. Churchwell
- S. Dieterich
- S. Dumalski
- S. Frullani
- S. Glamazdin
- S. I. Nagornyi
- S. I. Nagornyi
- S. J. Brodsky
- S. J. Brodsky
- S. J. Brodsky
- S. J. Freedman
- S. Malov
- S. Strauch
- T. Chang
- T. Gousset
- T. Kamae
- T. Kamae
- V. B. Ganenko
- V. Gorbenko
- V. Matveev
- V. P. Barannik
- V. Punjabi
- W. Liedemann
- W. Xu
- X. Jiang
- Y. Kang
- Z. Chai
- Z.-E. Meziani
- Publication venue
- 'American Physical Society (APS)'
- Publication date
- Field of study
Incorporating self-consistent single-particle potentials into the microscopic-macroscopic method
- Author
- A. Baran
- A. Idini
- A. Idini
- A. Parkhomenko
- A. Parkhomenko
- A. Sobiczewski
- A.N. Kuzmina
- A.P. Tonchev
- A.V. Afanasjev
- A.V. Afanasjev
- Ch. Theisen
- D. Ackermann
- D. Tarpanov
- D. Vautherin
- D. Vretenar
- E. Litvinova
- E. Litvinova
- E. Litvinova
- E. Litvinova
- E. Vigezzi
- F. Hofmann
- F.R. Xu
- G. G. Adamian
- G. Gori
- G.A. Lalazissis
- G.A. Lalazissis
- G.G. Adamian
- G.G. Adamian
- G.G. Adamian
- G.G. Adamian
- G.G. Adamian
- H. Lenske
- H. Lenske
- H. Liang
- I. Ahmad
- I. Ahmad
- I. Muntian
- I. Muntian
- I. Muntian
- I. Muntian
- J. Boguta
- J. Dechargé
- J. Dechargé
- J. Dudek
- J. Maruhn
- J. Meng
- J. Meng
- J. Meng
- J.J. Li
- J.W. Negele
- J.W. Negele
- Kun Wang
- L. A. Malov
- L.-G. Cuo
- M. Asai
- M. Baldo
- M. Baldo
- M. Bender
- M. Bender
- M. Bender
- M. Jaminon
- M.J. Martin
- M.J. Martin
- N. Tsoneva
- N. V. Antonenko
- N. Wang
- N.V. Antonenko
- P. Möller
- P. Ring
- R.V. Jolos
- S.-G. Zhou
- S.-G. Zhou
- S.-G. Zhou
- S.A. Fayans
- S.G. Nilsson
- S.P. Ivanova
- S.V. Tolokonnikov
- Shan-Gui Zhou
- T. Duguet
- T. Lisinski
- V. Derya
- V.A. Chepurnov
- V.G. Soloviev
- V.G. Soloviev
- V.M. Strutinsky
- V.V. Pashkevich
- W. Koepf
- W.-H. Long
- Z.-Y. Ma
- Z.-Y. Wu
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Influence of the shell effects on evaporation residue cross section of superheavy nuclei
- Author
- AJ Sierk
- AS Zubov
- AV Ignatyuk
- D Naderi
- D Naderi
- D Naderi
- D. Naderi
- FA Ivanyuk
- G Giardina
- GG Adamian
- GG Adamian
- GG Adamian
- J Hong
- J Töke
- JB Roberto
- JM Gates
- JR Nix
- K Nishio
- K Siwek-Wilczyńska
- KTR Davies
- L Zhu
- L Zhu
- M Brack
- MA Preston
- NV Antonenko
- P Fröbrich
- P Möller
- PN Nadtochy
- S Hofmann
- S. A. Alavi
- SG Nilsson
- T Asano
- VI Zagrebaev
- VI Zagrebaev
- VL Litnevsky
- VM Strutinsky
- W Loveland
- WJ Swiatecki
- WJ Swiatecki
- XJ Bao
- XJ Bao
- XJ Bao
- XJ Bao
- Y Aritomo
- Y Aritomo
- Y Jia
- YJ Liang
- YT Oganessian
- YT Oganessian
- Z Liu
- Z Min
- ZH Liu
- ZH Liu
- ZH Liu
- ZH Liu
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Superheavy Elements
- Author
- A. Ghiorso
- A. Ghiorso
- A. Ghiorso
- A. Ghiorso
- A. Sandulescu
- A. Sandulescu
- A. Sandulescu
- A. Sobiczewski
- A. TĂĽrler
- A. TĂĽrler
- A.B. Yakushev
- A.T. Kruppa
- A.V. Yeremin
- A.V. Yeremin
- B. Kadkhodayan
- B. Kindler
- B. Lommel
- B. Sulignano
- C. Stodel
- C.F.von Weizsäcker
- C.M. Folden III
- C.M. Folden III
- C.N. Davids
- Ch.E. DĂĽllmann
- D. Scharnweber
- D. Schumann
- D.C. Hoffman
- E. Kashy
- E.O. Fiset
- F.R. Xu
- G. Fazio
- G. Fazio
- G. Gamov
- G. Giardina
- G. MĂĽnzenberg
- G. MĂĽnzenberg
- G. MĂĽnzenberg
- G. MĂĽnzenberg
- G. MĂĽnzenberg
- G. MĂĽnzenberg
- G. MĂĽnzenberg
- G. MĂĽnzenberg
- G. MĂĽnzenberg
- G.A. Lalazissis
- G.G. Adamian
- G.G. Adamian
- G.G. Adamian
- G.G. Adamian
- G.G. Adamian
- G.G. Adamian
- G.N. Flerov
- G.T. Seaborg
- H. Folger
- H. Grawe
- H. Meldner
- I. Muntian
- I. Muntian
- I. Muntian
- I. Muntian
- I.V. Zagrebaev
- I.V. Zagrebaev
- J. Bossler
- J. Corish
- J. Grumann
- J. Hoffmann
- J. Maruhn
- J. Randrup
- J.-P. Delaroche
- J.F. Liang
- J.V. Kratz
- K. Morimoto
- K. Morita
- K. Morita
- K. Morita
- K. Morita
- K. Morita
- K. Nishio
- K. Rutz
- K.E. Gregorich
- K.H. Schmidt
- K.H. Schmidt
- L. Meitner
- M. Bender
- M. Bender
- M. Göppert-Mayer
- M. Leino
- M. Schädel
- M. Schädel
- M. Schädel
- M.G. Itkis
- M.R. Schmorak
- N. Angert
- O. Hahn
- O. Haxel
- P. Armbruster
- P. Armbruster
- P. Fröbrich
- P. Möller
- P. Möller
- P. Reiter
- P. Reiter
- P.A. Wilk
- R. Bass
- R. Eichler
- R. Eichler
- R. Eichler
- R. Eichler
- R. Geller
- R. Mann
- R. Mann
- R. Smolanczuk
- R. Smolanczuk
- R. Smolanczuk
- R.-D. Herzberg
- R.-D. Herzberg
- R.-D. Herzberg
- R.K. Gupta
- S. Bjørnholm
- S. Cwiok
- S. Cwiok
- S. Cwiok
- S. Eeckhaudt
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Hofmann
- S. Saro
- S.G. Nilsson
- S.K. Tandel
- S.L. Nelson
- T. Ichikawa
- T.N. Ginter
- U. Mosel
- U. Mosel
- V. Ninov
- V. Ninov
- V.I. Zagrebaev
- V.I. Zagrebaev
- V.I. Zagrebaev
- V.I. Zagrebaev
- V.V. Volkov
- V.Yu. Denisov
- V.Yu. Denisov
- V.Yu. Denisov
- W. Grimm
- W. Loveland
- W. Loveland
- W. Loveland
- W. Reisdorf
- W.D. Myers
- W.J. Swiatecki
- W.J. Swiatecki
- W.von Oertzen
- Y. Aritomo
- Yu.A. Lazarev
- Yu.A. Lazarev
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Yu.Ts. Oganessian
- Z. Patyk
- Z.G. Gan
- Z.G. Gan
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2009
- Field of study
Membrane Depth-Dependent Energetic Contribution of the Tryptophan Side Chain to the Stability of Integral Membrane Proteins
- Author
- Adamian L.
- Bowie J. U.
- Cho W. H.
- de Planque M. R.
- Dennis Rinehart
- Dill K. A.
- Eisenberg D.
- Ellena J. F.
- Engelman D. M.
- Fersht A. R.
- Gleason N. J.
- Heedeok Hong
- Hessa T.
- Hessa T.
- Hong H.
- Hong H.
- Huysmans G. H.
- Jayasinghe S.
- Killian J. A.
- Kleinschmidt J. H.
- Kleinschmidt J. H.
- Kyte J.
- Lai A. L.
- Landolt-Marticorena C.
- Liang B.
- Lukas K. Tamm
- Moon C. P.
- Nozaki Y.
- Ojemalm K.
- Pautsch A.
- Popa A.
- Prilipov A.
- Rodionova N. A.
- Sanchez K. M.
- Schramm C. A.
- Senes A.
- Shortle D.
- Shortle D.
- Snider C.
- Tafer H.
- Tusnady G. E.
- Ulmschneider M. B.
- Uversky V. N.
- White S. H.
- Wimley W. C.
- Wimley W. C.
- Wimley W. C.
- Yau W. M.
- Publication venue
- 'American Chemical Society (ACS)'
- Publication date
- Field of study
Engineering Phage Materials with Desired Peptide Display: Rational Design Sustained through Natural Selection
- Author
- Adamian L.
- Bermudez H.
- Brammer L. A.
- Braun P.
- Brissette R.
- Chen G.
- Choo K. H.
- Choo K. H.
- Click E. M.
- Dogic Z.
- Elf J.
- Feng J. N.
- Feng J. N.
- Frenkel D.
- Genin S.
- Hajitou A.
- Hohn B.
- Hohn B.
- Huang Y.
- Iannolo G.
- Imai S.
- Jain R. G.
- Jaworski J. W.
- Kolb G.
- Krag D. N.
- Kuhn A.
- Kuhn A.
- Kuzmicheva G. A.
- Lee S. K.
- Lee S. W.
- Lee S. W.
- Li R.
- Liang J.
- Makowski L.
- Malik P.
- Marvin D. A.
- Merzlyak A.
- Merzlyak A.
- Nam K. T.
- Nikaido H.
- Nikaido H.
- Noren K. A.
- Opalka N.
- Papavoine C. H. M.
- Petrenko V. A.
- Petrenko V. A.
- Pierschbacher M. D.
- Pratt D.
- Rodi D. J.
- Rodi D. J.
- Ruoslahti E.
- Russel M.
- Russel M.
- Sambrook J.
- Samuelson J. C.
- Samuelson J. C.
- Schense J. C.
- Schuenemann T. A.
- Sephel G. C.
- Silva G. A.
- Smith G. P.
- Smith G. P.
- Stopar D.
- Stopar D.
- Uchida M.
- Vilette D.
- von Heijne G.
- Wang Y. A.
- Whaley S. R.
- Yamashita I.
- Zilberstein D.
- Zlotnick A.
- Publication venue
- 'American Chemical Society (ACS)'
- Publication date
- Field of study
RosettaTMH: a method for membrane protein structure elucidation combining EPR distance restraints with assembly of transmembrane helices
- Author
- Adamian L Liang J
- Alexander N Al-Mestarihi A, Bortolus M, et al.
- Alexander NS Stein RA, Koteiche HA, et al.
- Altenbach C Cai K, Klein-Seetharaman J, et al.
- Baker LA Baldus M
- Bakheet TM Doig AJ
- Barth P Schonbrun J, Baker D
- Barth P Wallner B, Baker D
- Beasley KN Sutch BT, Hatmal MM, et al.
- Berman HM Battistuz T, Bhat TN, et al.
- Berman HM Westbrook J, Feng Z, et al.
- Chun E Thompson AA, Liu W, et al.
- Combs SA Deluca SL, Deluca SH, et al.
- Dimaio F Leaver-Fay A, Bradley P, et al.
- Faham S Watanabe A, Besserer GM, et al.
- Fanucci GE Cafiso DS
- Fischer AW Alexander NS, Woetzel N, et al.
- Fiser A Sali A
- Gregory KJ Nguyen ED, Reiff SD, et al.
- Hagelueken G Ward R, Naismith JH, et al.
- Hatmal MM Li Y, Hegde BG, et al.
- Hirst SJ Alexander N, Mchaourab HS, et al.
- Hopf TA Colwell LJ, Sheridan R, et al.
- Hopkins AL Groom CR
- Horst R Stanczak P, Stevens RC, et al.
- Hubbell WL McHaourab HS, Altenbach C, et al.
- Islam SM Stein RA, McHaourab HS, et al.
- Jeschke G Chechik V, Ionita P, et al.
- Karakas M Woetzel N, Staritzbichler R, et al.
- Kazmier K Alexander NS, Meiler J, et al.
- Kazmier K Sharma S, Quick M, et al.
- Klammt C Maslennikov I, Bayrhuber M, et al.
- Krishnamurthy H Gouaux E
- Kroeze WK Sheffler DJ, Roth BL
- Leaver-Fay A Tyka M, Lewis SM, et al.
- Liu W Wacker D, Gati C, et al.
- Liu YS Sompornpisut P, Perozo E
- Ma D Lu P, Yan C, et al.
- Maslennikov I Choe S
- Mchaourab HS Steed PR, Kazmier K
- Metropolis N Rosenbluth A, Rosenbluth M, et al.
- Metropolis NU Ulam S
- Misura KM Baker D
- Misura KM Chivian D, Rohl CA, et al.
- Ni QZ Daviso E, Can TV, et al.
- Nugent T Jones DT
- Nugent T Jones DT
- Overington JP Al-Lazikani B, Hopkins AL
- Perez C Koshy C, Yildiz O, et al.
- Perozo E Cortes DM, Cuello LG
- Rohl CA Strauss CE, Misura KM, et al.
- Rohl CA Strauss CEM, Chivian D, et al.
- Roy A Kucukural A, Zhang Y
- Sali A Blundell TL
- Schwede T Kopp J, Guex N, et al.
- Simons KT Kooperberg C, Huang E, et al.
- Tang M Comellas G, Rienstra CM
- Tusnady GE Dosztanyi Z, Simon I
- Tyka MD Jung K, Baker D
- Viklund H Elofsson A
- Webb B Sali A
- Weiner BE Woetzel N, Karakas M, et al.
- Woetzel N Karakas M, Staritzbichler R, et al.
- Yamashita A Singh SK, Kawate T, et al.
- Zhang Y
- Zou P McHaourab HS
- Zou P Mchaourab HS
- Publication venue
- 'American Institute of Mathematical Sciences (AIMS)'
- Publication date
- 01/01/2015
- Field of study