-
1
-
-
84860369376
-
Structural basis for the regulation of protein kinase A by activation loop phosphorylation
-
Steichen JM, Kuchinskas M, Keshwani MM, Yang J, Adams JA, Taylor SS (2012) Structural basis for the regulation of protein kinase A by activation loop phosphorylation. J Biol Chem 287:14672-14680.
-
(2012)
J Biol Chem
, vol.287
, pp. 14672-14680
-
-
Steichen, J.M.1
Kuchinskas, M.2
Keshwani, M.M.3
Yang, J.4
Adams, J.A.5
Taylor, S.S.6
-
2
-
-
0038823633
-
Molecular recognition in Helix-Loop-Helix and Helix-Loop-Helix-Leucine zipper domains
-
Ciarapica R, Rosati J, Cesareni G, Nasi S (2003) Molecular recognition in Helix-Loop-Helix and Helix-Loop-Helix-Leucine zipper domains. J Biol Chem 278:12182-12190.
-
(2003)
J Biol Chem
, vol.278
, pp. 12182-12190
-
-
Ciarapica, R.1
Rosati, J.2
Cesareni, G.3
Nasi, S.4
-
3
-
-
2442717874
-
q/11α signaling
-
DOI 10.1074/jbc.M312407200
-
Bernstein LS, Ramineni S, Hague C, Cladman W, Chidiac P, Levey AI, Hepler JR (2004) RGS2 binds directly and selectively to the Ml muscarinic acetylcholine receptor third intracellular loop to modulate Gq/llalpha signaling. J Biol Chem 279:21248-21256. (Pubitemid 38656530)
-
(2004)
Journal of Biological Chemistry
, vol.279
, Issue.20
, pp. 21248-21256
-
-
Bernstein, L.S.1
Ramineni, S.2
Hague, C.3
Cladman, W.4
Chidiac, P.5
Levey, A.I.6
Hepler, J.R.7
-
4
-
-
33750982413
-
Antibody binding loop insertions as diversity elements
-
Kiss C, Fisher H, Pesavento E, Dai M, Valero R, Ovecka M, Nolan R, Phipps ML, Velappan N, Chasteen L, Martinez JS, Pavlik P, Bradbury AR (2006) Antibody binding loop insertions as diversity elements. Nucl Acids Res 34:132-146.
-
(2006)
Nucl Acids Res
, vol.34
, pp. 132-146
-
-
Kiss, C.1
Fisher, H.2
Pesavento, E.3
Dai, M.4
Valero, R.5
Ovecka, M.6
Nolan, R.7
Phipps, M.L.8
Velappan, N.9
Chasteen, L.10
Martinez, J.S.11
Pavlik, P.12
Bradbury, A.R.13
-
5
-
-
0022527184
-
α-Lactalbumin possesses a novel calcium binding loop
-
Stuart D, Acharya K, Walker N, Smith S, Lewis M, Phillips D (1986) Lactalbumin possesses a novel calcium binding loop. Nature 324:84-87. (Pubitemid 16008423)
-
(1986)
Nature
, vol.324
, Issue.6092
, pp. 84-87
-
-
Stuart, D.I.1
Acharya, K.R.2
Walker, N.P.C.3
-
7
-
-
0027445510
-
The S4-S5 loop contributes to the ion-selective pore of potassium channels
-
DOI 10.1016/0896-6273(93)90083-4
-
Slesinger PA, Jan YN, Jan LY (1993) The S4-S5 loop contributes to the ion-selective pore of potassium channels. Neuron 11(4):739-749. (Pubitemid 23321781)
-
(1993)
Neuron
, vol.11
, Issue.4
, pp. 739-749
-
-
Slesinger, P.A.1
Yuh Nung Jan2
Lily Yeh Jan3
-
8
-
-
0034567501
-
Ab initio loop modeling and its application to homology modeling
-
Bruccoleri RE (2000) Ab initio loop modeling and its application to homology modeling. Methods in Molecular Biology 143:247-264.
-
(2000)
Methods in Molecular Biology
, vol.143
, pp. 247-264
-
-
Bruccoleri, R.E.1
-
9
-
-
34748913195
-
The rigid connecting loop stabilizes hairpin folding of the two helices of the ATP synthase subunit c
-
DOI 10.1110/ps.072776307
-
Dmitriev OY, Fillingame RH (2007) The rigid connecting loop stabilizes hairpin folding of the two helices of the ATP synthase subunit c. Protein Sci 16(10):2118-2122. (Pubitemid 47481647)
-
(2007)
Protein Science
, vol.16
, Issue.10
, pp. 2118-2122
-
-
Dmitriev, O.Y.1
Fillingame, R.H.2
-
11
-
-
33748684383
-
Identification of function-associated loop motifs and application to protein function prediction
-
DOI 10.1093/bioinformatics/btl382
-
Espadaler J, Querol E, Aviles FX, Oliva B (2006) Identification of function-associated loop motifs and application to protein function prediction. Bioinformatics, 22(18):2237-2243. (Pubitemid 44390878)
-
(2006)
Bioinformatics
, vol.22
, Issue.18
, pp. 2237-2243
-
-
Espadaler, J.1
Querol, E.2
Aviles, F.X.3
Oliva, B.4
-
12
-
-
26944443142
-
Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels
-
Tasneem A, Iyer LM, Jakobsson E, Aravind L (2005) Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels. Genome Biol 6 (1) R4.
-
(2005)
Genome Biol
, vol.6
, Issue.1
-
-
Tasneem, A.1
Iyer, L.M.2
Jakobsson, E.3
Aravind, L.4
-
15
-
-
41549100710
-
Determination of conformational preferences of dipeptides using vibrational spectroscopy
-
DOI 10.1021/jp7096313
-
Grdadolnik J, Grdadolnik SG, Avbelj F (2008) Determination of conformational preferences of dipeptides using vibrational spectroscopy. J Phys Chem B 112:2712-2718. (Pubitemid 351472981)
-
(2008)
Journal of Physical Chemistry B
, vol.112
, Issue.9
, pp. 2712-2718
-
-
Grdadolnik, J.1
Grdadolnik, S.G.2
Avbelj, F.3
-
16
-
-
15244362640
-
Structural similarity of loops in protein families: Toward the understanding of protein evolution
-
Panchenko AR, Madej T (2005) Structural similarity of loops in protein families: toward the understanding of protein evolution. BMC Evol Biol 5:10.
-
(2005)
BMC Evol Biol
, vol.5
, pp. 10
-
-
Panchenko, A.R.1
Madej, T.2
-
17
-
-
77149152176
-
Backbone statistical potential from local sequence-structure interactions in protein loops
-
Rata I, Li Y, Jakobsson E (2010) Backbone Statistical Potential from Local Sequence-Structure Interactions in Protein Loops. J Phys Chem B 114(5):1859-1869.
-
(2010)
J Phys Chem B
, vol.114
, Issue.5
, pp. 1859-1869
-
-
Rata, I.1
Li, Y.2
Jakobsson, E.3
-
18
-
-
0001079105
-
On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations
-
Kabsch W, Sander C (1983) On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations. Proc Natl Acad Sci USA 81:1075-1081.
-
(1983)
Proc Natl Acad Sci USA
, vol.81
, pp. 1075-1081
-
-
Kabsch, W.1
Sander, C.2
-
19
-
-
0027448801
-
Origins of structural diversity within sequentially identical hexapeptides
-
Cohen BI, Presnell SR, Cohen FE (1993) Origins of structural diversity within sequentially identical hexapeptides. Protein Sci 2:2134-2145. (Pubitemid 23354716)
-
(1993)
Protein Science
, vol.2
, Issue.12
, pp. 2134-2145
-
-
Cohen, B.I.1
Presnell, S.R.2
Cohen, F.E.3
-
20
-
-
13944275960
-
The protein coil library: A structural database of nonhelix, nonstrand fragments derived from the PDB
-
DOI 10.1002/prot.20394
-
Fitzkee NC, Fleming PJ, Rose GD (2005) The Protein Coil Library: a structural database of nonhelix, nonstrand fragments derived from the PDB. Proteins 58(4):852-854. (Pubitemid 40271250)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.58
, Issue.4
, pp. 852-854
-
-
Fitzkee, N.C.1
Fleming, P.J.2
Rose, G.D.3
-
21
-
-
0043180474
-
PISCES: A protein sequence culling server
-
DOI 10.1093/bioinformatics/btg224
-
Wang G, Dunbrack RL (2003) PISCES: a protein sequence culling server. Bioinformatics 19(12):1589-1591. (Pubitemid 37038881)
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
22
-
-
0019028066
-
Model for haptoglobin heavy chain based upon structural homology
-
Greer J (1980) Model for haptoglobin heavy chain based upon structural homology. Proc Natl Acad Sci USA 77:3393-3397.
-
(1980)
Proc Natl Acad Sci USA
, vol.77
, pp. 3393-3397
-
-
Greer, J.1
-
23
-
-
0026530262
-
Taxonomy and conformational analysis of loops in proteins
-
Ring CS, Kneller DG, Langridge R, Cohen FE (1992) Taxonomy and conformational analysis of loops in proteins. J Mol Biol 224(3):685-699.
-
(1992)
J Mol Biol
, vol.224
, Issue.3
, pp. 685-699
-
-
Ring, C.S.1
Kneller, D.G.2
Langridge, R.3
Cohen, F.E.4
-
24
-
-
0026696412
-
Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations
-
Tramontano A, Lesk AM (1992) Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations. Proteins, 13:231-245.
-
(1992)
Proteins
, vol.13
, pp. 231-245
-
-
Tramontano, A.1
Lesk, A.M.2
-
26
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181(4096):223-230.
-
(1973)
Science
, vol.181
, Issue.4096
, pp. 223-230
-
-
Anfinsen, C.B.1
-
27
-
-
0031021792
-
A fast and efficient program for modeling protein loops
-
Zhang H, Lai L, Han Y, Tang Y (1997) A Fast and Efficient Program for Modeling Protein Loops. Biopolymers 41:61-72.
-
(1997)
Biopolymers
, vol.41
, pp. 61-72
-
-
Zhang, H.1
Lai, L.2
Han, Y.3
Tang, Y.4
-
28
-
-
56549099908
-
Prediction of protein loop structures using a local move Monte Carlo approach and a gridbased force field
-
Cui M, Mezei M, Osman R (2008) Prediction of Protein Loop Structures using a Local Move Monte Carlo Approach and a Gridbased Force Field. Protein Eng Des Sel 21(12):729-735.
-
(2008)
Protein Eng Des Sel
, vol.21
, Issue.12
, pp. 729-735
-
-
Cui, M.1
Mezei, M.2
Osman, R.3
-
29
-
-
0033135619
-
Prediction of loop geometries using a generalized born model of solvation effects
-
DOI 10.1002/(SICI)1097-0134(19990501)35:2<173: :AID-PROT4>3.0.CO;2- 2
-
Rapp CS, Friesner RA (1999) Prediction of loop geometries using a generalized born model of solvation effects. Proteins 35:173-183. (Pubitemid 29165131)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.35
, Issue.2
, pp. 173-183
-
-
Rapp, C.S.1
Friesner, R.A.2
-
30
-
-
0037375615
-
Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized born solvation model
-
DOI 10.1002/prot.10235
-
de Bakker P I W, Depristo MA, Burke DF, Blundell TL (2003) Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model. Proteins 51:21-40. (Pubitemid 36293030)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.51
, Issue.1
, pp. 21-40
-
-
De Bakker, P.I.W.1
DePristo, M.A.2
Burke, D.F.3
Blundell, T.L.4
-
31
-
-
0029011701
-
A second generation force-field for the simulation of proteins, nucleicacids, and organic-molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM (1995) A second generation force-field for the simulation of proteins, nucleicacids, and organic-molecules. J Am Chem Soc 117:5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
-
32
-
-
39749085824
-
LOOPER: A molecular mechanics-based algorithm for protein loop prediction
-
DOI 10.1093/protein/gzm083
-
Spassov VZ, Flook PK, Yan L (2008) LOOPER: a molecular mechanics-based algorithm for protein loop prediction. Protein Eng Des Sel 21(2):91-100. (Pubitemid 351301921)
-
(2008)
Protein Engineering, Design and Selection
, vol.21
, Issue.2
, pp. 91-100
-
-
Spassov, V.Z.1
Flook, P.K.2
Yan, L.3
-
33
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization and dynamics calculations. J Comput Chem 4:187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
34
-
-
1842532008
-
A hierarchical approach to all-atom protein loop prediction
-
DOI 10.1002/prot.10613
-
Jacobson MP, Pincus DL, Rapp CS, Day T J F, Honig B, Shaw DE, Friesner RA (2004) A Hierarchical Approach to All-atom Protein Loop Prediction. Proteins 55:351-367. (Pubitemid 38437493)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.55
, Issue.2
, pp. 351-367
-
-
Jacobson, M.P.1
Pincus, D.L.2
Rapp, C.S.3
Day, T.J.F.4
Honig, B.5
Shaw, D.E.6
Friesner, R.A.7
-
35
-
-
0042296402
-
OPLS all-atom force field for carbohydrates
-
Damm W, Frontera A, Tirado-Rives J, Jorgensen WL (1997) OPLS All-Atom Force Field for Carbohydrates. J Comput Biol 18(16):1955-1970. (Pubitemid 127598549)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.16
, pp. 1955-1970
-
-
Damm, W.1
Frontera, A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
36
-
-
34548331699
-
Prediction of protein loop geometries in solution
-
DOI 10.1002/prot.21503
-
Rapp CS, Strauss T, Nederveen A, Fuentes G (2007) Prediction of protein loop geometries in solution. Proteins 69:69-74. (Pubitemid 47339140)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.69
, Issue.1
, pp. 69-74
-
-
Rapp, C.S.1
Strauss, T.2
Nederveen, A.3
Fuentes, G.4
-
37
-
-
33748988479
-
Long loop prediction using the protein local optimization program
-
DOI 10.1002/prot.21040
-
Zhu K, Pincus DL, Zhao S, Friesner RA (2006) Long Loop Prediction Using the Protein Local Optimization Program. Proteins 65:438-452. (Pubitemid 44454115)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.2
, pp. 438-452
-
-
Zhu, K.1
Pincus, D.L.2
Zhao, S.3
Friesner, R.A.4
-
38
-
-
58149157667
-
Prediction of protein loop conformation using the AGBNP implicit solvent model and torsion angle sampling
-
Felts AK, Gallicchio E, Chekmarev D, Paris KA, Friesner RA, Levy RM (2008) Prediction of Protein Loop Conformation Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. J Chem Theory Comput 4(5):855-868.
-
(2008)
J Chem Theory Comput
, vol.4
, Issue.5
, pp. 855-868
-
-
Felts, A.K.1
Gallicchio, E.2
Chekmarev, D.3
Paris, K.A.4
Friesner, R.A.5
Levy, R.M.6
-
39
-
-
1442330396
-
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
-
Gallicchio E, Levy RM (2004) AGBNP: An Analytic Implicit Solvent Model Suitable for Molecular Dynamics Simulations and High-Resolution Modeling. J Comput Chem 25:479-499.
-
(2004)
J Comput Chem
, vol.25
, pp. 479-499
-
-
Gallicchio, E.1
Levy, R.M.2
-
40
-
-
47349128896
-
Toward better refinement of comparative models: Predicting loops in inexact environments
-
DOI 10.1002/prot.21990
-
Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP (2008) Toward better refinement of comparative models: predicting loops in inexact environments. Proteins 72(3):959-971. (Pubitemid 352000873)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.72
, Issue.3
, pp. 959-971
-
-
Sellers, B.D.1
Zhu, K.2
Zhao, S.3
Friesner, R.A.4
Jacobson, M.P.5
-
41
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
DOI 10.1021/ar000033j
-
Kollman PA, Massova I, Reyes C, Kuhn B, Huo SH, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Srinivasan J, Case DA, Cheatham TE (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts Chem Res 33(12):889-897. (Pubitemid 32056774)
-
(2000)
Accounts of Chemical Research
, vol.33
, Issue.12
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
-
42
-
-
15244349255
-
Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation
-
DOI 10.1110/ps.041004105
-
Fogolari F, Tosatto S C E (2005) Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation. Protein Sci 14(4):889-901. (Pubitemid 40389358)
-
(2005)
Protein Science
, vol.14
, Issue.4
, pp. 889-901
-
-
Fogolari, F.1
Tosatto, S.C.E.2
-
43
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl MJ (1990) Calculation of conformational ensembles from potentials of mean force - an approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213:859-883. (Pubitemid 20213222)
-
(1990)
Journal of Molecular Biology
, vol.213
, Issue.4
, pp. 859-883
-
-
Sippl, M.J.1
-
44
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
DOI 10.1110/ps.0217002
-
Zhou H, Zhou Y (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 11:2714-2726. (Pubitemid 35191145)
-
(2002)
Protein Science
, vol.11
, Issue.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
45
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
DOI 10.1110/ps.062416606
-
Shen M, Sali A (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15(11):2507-2524. (Pubitemid 44771688)
-
(2006)
Protein Science
, vol.15
, Issue.11
, pp. 2507-2524
-
-
Shen, M.-Y.1
Sali, A.2
-
46
-
-
46449132707
-
Specific interactions for ab initio folding of protein terminal regions with secondary structures
-
DOI 10.1002/prot.21968
-
Yang Y, Zhou Y (2008) Specific interactions for ab Initio folding of protein terminal regions with secondary structures. Proteins 72:793-803. (Pubitemid 351928531)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.72
, Issue.2
, pp. 793-803
-
-
Yang, Y.1
Zhou, Y.2
-
47
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser A, Do R K G, Sali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753-1773.
-
(2000)
Protein Sci
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.G.2
Sali, A.3
-
48
-
-
2442449534
-
Modeling structurally variable regions in homologous proteins with rosetta
-
DOI 10.1002/prot.10629
-
Rohl RA, Strauss CE, Chivian D, Baker D (2004) Modeling structurally variable regions in homologous proteins with Rosetta. Proteins 55:656-677. (Pubitemid 38620090)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.55
, Issue.3
, pp. 656-677
-
-
Rohl, C.A.1
Strauss, C.E.M.2
Chivian, D.3
Baker, D.4
-
49
-
-
68349104348
-
Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
-
Mandell DJ, Coutsias EA, Kortemme T (2009) Sub-Angstrom Accuracy in Protein Loop Reconstruction by Robotics-Inspired Conformational Sampling. Nat Methods 6:551-552.
-
(2009)
Nat Methods
, vol.6
, pp. 551-552
-
-
Mandell, D.J.1
Coutsias, E.A.2
Kortemme, T.3
-
50
-
-
0032612579
-
Ab initio protein structure prediction of CASP III targets using ROSETTA
-
DOI 10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z
-
Simons KT, Bonneau R, Ruczinski I, Baker D (1999) Ab initio protein structure prediction of CASP III targets using Rosetta. Proteins 37(S3):171-176. (Pubitemid 29463528)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.37
, Issue.SUPPL. 3
, pp. 171-176
-
-
Simons, K.T.1
Bonneau, R.2
Ruczinski, I.3
Baker, D.4
-
52
-
-
0027208831
-
Modeling of protein loops by simulated annealing
-
Collura V, Higo J, Gamier J (1993) Modeling of protein loops by simulated annealing. Protein Sci 2:1502-1510. (Pubitemid 23262843)
-
(1993)
Protein Science
, vol.2
, Issue.9
, pp. 1502-1510
-
-
Collura, V.1
Higo, J.2
Garnier, J.3
-
53
-
-
0000781576
-
Exact analytical loop closure in proteins using polynomial equations
-
Wedemeyer WJ, Scheraga HA (1999) Exact Analytical Loop Closure in Proteins Using Polynomial Equations. J Comput Chem 20(8):819-844. (Pubitemid 129656130)
-
(1999)
Journal of Computational Chemistry
, vol.20
, Issue.8
, pp. 819-844
-
-
Wedemeyer, W.J.1
Scheraga, H.A.2
-
55
-
-
0023478807
-
Predicting antobody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures
-
Shenkin S, Yarmush DL, Fine RM, Wang H, Levinthal C (1987) Predicting antobody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures. Biopolymers 26:2053-2085.
-
(1987)
Biopolymers
, vol.26
, pp. 2053-2085
-
-
Shenkin, S.1
Yarmush, D.L.2
Fine, R.M.3
Wang, H.4
Levinthal, C.5
-
56
-
-
0038115250
-
On the kinematics of protein folding
-
Cahill S, Cahill M, Cahill K (2003) On the kinematics of protein folding. J Comput Chem 24:1364-1370.
-
(2003)
J Comput Chem
, vol.24
, pp. 1364-1370
-
-
Cahill, S.1
Cahill, M.2
Cahill, K.3
-
57
-
-
0037406075
-
Cyclic coordinate descent: A robotics algorithm for protein loop closure
-
DOI 10.1110/ps.0242703
-
Canutescu AA, Dunbrack RL (2003) Cyclic Coordinate Descent: A Robotics Algorithm for Protein Loop Closure. Protein Sci 12:963-972. (Pubitemid 36505431)
-
(2003)
Protein Science
, vol.12
, Issue.5
, pp. 963-972
-
-
Canutescu, A.A.1
Dunbrack Jr., R.L.2
-
58
-
-
13444304144
-
Inverse kinematics in biology: The protein loop closure problem
-
DOI 10.1177/0278364905050352, Robotics Techniques Applied to Computational Biology
-
Kolodny R, Guibas L, Levitt M, Koehl P (2005) Inverse Kinematics in Biology: The Protein Loop Closure Problem. Int J Robot Res 24:151-163. (Pubitemid 40207003)
-
(2005)
International Journal of Robotics Research
, vol.24
, Issue.2-3
, pp. 151-163
-
-
Kolodny, R.1
Guibas, L.2
Levitt, M.3
Koehl, P.4
-
59
-
-
25444455574
-
Full cyclic coordinate descent: Solving the protein loop closure problem in Ca space
-
Boomsma W, Hamelryck T (2005) Full cyclic coordinate descent: solving the protein loop closure problem in Ca space. BMC Bioinformatics 6:159.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 159
-
-
Boomsma, W.1
Hamelryck, T.2
-
60
-
-
38549154569
-
Loop modeling: Sampling, filtering, and scoring
-
DOI 10.1002/prot.21612
-
Soto CS, Fasnacht M, Zhu J, Forrest L, Honig B (2008) Loop modelling: sampling, filtering, and scoring. Proteins 70:834-843. (Pubitemid 351161942)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.70
, Issue.3
, pp. 834-843
-
-
Soto, C.S.1
Fasnacht, M.2
Zhu, J.3
Forrest, L.4
Honig, B.5
-
62
-
-
77954679017
-
Improving predicted protein loop structure ranking using a pareto-optimality consensus method
-
Li Y, Rata I, Chiu S, Jakobsson E (2010) Improving Predicted Protein Loop Structure Ranking using a Pareto-Optimality Consensus Method. BMC Struct Biol 10:22.
-
(2010)
BMC Struct Biol
, vol.10
, pp. 22
-
-
Li, Y.1
Rata, I.2
Chiu, S.3
Jakobsson, E.4
-
63
-
-
79955906529
-
Assessing protein loop flexibility by hierarchical Monte Carlo sampling
-
Nilmeier J, Hua L, Coutsias EA, Jacobson MP (2011) Assessing protein loop flexibility by hierarchical Monte Carlo sampling. J Chem Theory Comput 7(5):1564-1574.
-
(2011)
J Chem Theory Comput
, vol.7
, Issue.5
, pp. 1564-1574
-
-
Nilmeier, J.1
Hua, L.2
Coutsias, E.A.3
Jacobson, M.P.4
-
65
-
-
0034870539
-
Ab initio modeling of small, medium, and large loops in proteins
-
DOI 10.1002/1097-0282(2001)60:2<153: :AID-BIP1010>3.0.CO;2-6
-
Galaktionov S, Nikiforovich GV, Marshall GR (2001) Ab initio modelling of small, medium, and large loops in proteins. Peptide Science 60(2):153-168. (Pubitemid 32743531)
-
(2001)
Biopolymers - Peptide Science Section
, vol.60
, Issue.2
, pp. 153-168
-
-
Galaktionov, S.1
Nikiforovich, G.V.2
Marshall, G.R.3
-
66
-
-
0037375742
-
Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles
-
DOI 10.1002/prot.10285
-
DePristo MA, de Bakker P I W, Lovell SC, Blundell TL (2003) Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins 51(1):41-55. (Pubitemid 36293031)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.51
, Issue.1
, pp. 41-55
-
-
DePristo, M.A.1
De Bakker, P.I.W.2
Lovell, S.C.3
Blundell, T.L.4
-
67
-
-
40549088876
-
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions
-
DOI 10.1002/jcc.20827
-
Olson MA, Feig M, Brooks CL (2008) Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J Comput Chem 29(5):820-831. (Pubitemid 351364856)
-
(2008)
Journal of Computational Chemistry
, vol.29
, Issue.5
, pp. 820-831
-
-
Olson, M.A.1
Feig, M.2
Brooks III, C.L.3
-
68
-
-
0001056843
-
Efficient Monte Carlo methods for cyclic peptides
-
Wu M, Deem MW (1999) Efficient Monte Carlo methods for cyclic peptides. Mol Phys 97:559-580. (Pubitemid 129707886)
-
(1999)
Molecular Physics
, vol.97
, Issue.4
, pp. 559-580
-
-
Wu, M.G.1
Deem, M.W.2
-
69
-
-
0034847744
-
Improved protein loop prediction from sequence alone
-
Burke DF, Deane CM (2001) Improved protein loop prediction from sequence alone. Protein Eng 14(7):473-478. (Pubitemid 32846932)
-
(2001)
Protein Engineering
, vol.14
, Issue.7
, pp. 473-478
-
-
Burke, D.F.1
Deane, C.M.2
-
70
-
-
85005670823
-
Conformational sampling of loop structures using genetic algorithms
-
Ring CS, Cohen FE (1994) Conformational sampling of loop structures using genetic algorithms. Israel Journal of Chemistry 34:245-252.
-
(1994)
Israel Journal of Chemistry
, vol.34
, pp. 245-252
-
-
Ring, C.S.1
Cohen, F.E.2
-
71
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of State Calculations by Fast Computing Machines. J Chem Phys 21:1087-1092.
-
(1953)
J Chem Phys
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
72
-
-
79960711882
-
Sampling multiple scoring functions can improve protein loop structure prediction accuracy
-
Li Y, Rata I, Jakobsson E (2011) Sampling Multiple Scoring Functions Can Improve Protein Loop Structure Prediction Accuracy. J Chem Inf Model 51(7):1656-1666.
-
(2011)
J Chem Inf Model
, vol.51
, Issue.7
, pp. 1656-1666
-
-
Li, Y.1
Rata, I.2
Jakobsson, E.3
-
73
-
-
84910138210
-
MOMCMC: An efficient Monte Carlo method for multi-objective sampling over real parameter space
-
Li Y (2012) MOMCMC: An Efficient Monte Carlo Method for Multi-objective sampling over real parameter space. Comput Math Appl. 64:3542-3556.
-
(2012)
Comput Math Appl
, vol.64
, pp. 3542-3556
-
-
Li, Y.1
-
74
-
-
77949434706
-
Modeling of loops in proteins: A multimethod approach
-
Jamroz M, Kolinski A (2010) Modeling of loops in proteins: a multimethod approach. BMC Struct Biol 10:5.
-
(2010)
BMC Struct Biol
, vol.10
, pp. 5
-
-
Jamroz, M.1
Kolinski, A.2
-
75
-
-
78349284741
-
Protein loop modeling by using fragment assembly and analytical loop closure
-
Lee J, Lee D, Park H, Coutsias EA, Seok C (2010) Protein loop modeling by using fragment assembly and analytical loop closure. Proteins 78:3428-3436.
-
(2010)
Proteins
, vol.78
, pp. 3428-3436
-
-
Lee, J.1
Lee, D.2
Park, H.3
Coutsias, E.A.4
Seok, C.5
-
76
-
-
0035107308
-
CODA: A combined algorithm for predicting the structurally variable regions of protein models
-
DOI 10.1110/ps.37601
-
Deane CM, Blundell TL (2001) CODA: a combined algorithm for predicting the structurally variable regions of protein models. Protein Sci 10:599-612. (Pubitemid 32221148)
-
(2001)
Protein Science
, vol.10
, Issue.3
, pp. 599-612
-
-
Deane, C.M.1
Blundell, T.L.2
-
77
-
-
77949561118
-
Mining protein loops using a structural alphabet and statistical exceptionality
-
Regad L, Martin J, Nuel G, Camproux A (2010) Mining protein loops using a structural alphabet and statistical exceptionality. BMC Bioinformatics 11:75.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 75
-
-
Regad, L.1
Martin, J.2
Nuel, G.3
Camproux, A.4
-
78
-
-
0002336164
-
Ring closure and local conformational deformations of chain molecules
-
Go N, Scheraga H (1970) Ring closure and local conformational deformations of chain molecules. Macromolecules 3:178-187.
-
(1970)
Macromolecules
, vol.3
, pp. 178-187
-
-
Go, N.1
Scheraga, H.2
-
79
-
-
80052575512
-
Progress in super long loop prediction
-
Zhao S, Zhu K, Li J, Friesner RA (2011) Progress in super long loop prediction. Proteins 79:2920-2935.
-
(2011)
Proteins
, vol.79
, pp. 2920-2935
-
-
Zhao, S.1
Zhu, K.2
Li, J.3
Friesner, R.A.4
-
80
-
-
83555177246
-
Predicting flexible loop regions that interact with ligands: The challenge of accurate scoring
-
Danielson ML, Lill MA (2012) Predicting flexible loop regions that interact with ligands: the challenge of accurate scoring. Proteins 80:246-260.
-
(2012)
Proteins
, vol.80
, pp. 246-260
-
-
Danielson, M.L.1
Lill, M.A.2
-
81
-
-
36749039234
-
High-resolution design of a protein loop
-
DOI 10.1073/pnas.0707977104
-
Hu X, Wang H, Ke H, Kuhlman B (2007) High-resolution design of a protein loop. Proc Natl Acad Sci USA 104:17668-17673. (Pubitemid 350210892)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.45
, pp. 17668-17673
-
-
Hu, X.1
Wang, H.2
Ke, H.3
Kuhlman, B.4
-
82
-
-
0027141511
-
A structure refinement method based on molecular dynamics in four spatial dimensions
-
DOI 10.1006/jmbi.1993.1624
-
van Schaik RC, Berendsen H J C, Torda AE, van Gunsteren WF (1993) A structure refinement method based on molecular dynamics in four spatial dimensions. J. Mol. Biol. 234:751-762. (Pubitemid 24007799)
-
(1993)
Journal of Molecular Biology
, vol.234
, Issue.3
, pp. 751-762
-
-
Van Schaik, R.C.1
Berendsen, H.J.C.2
Torda, A.E.3
Van Gunsteren, W.F.4
-
83
-
-
0037941126
-
Generation of accurate protein loop conformations through low-barrier molecular dynamics
-
DOI 10.1002/prot.10363
-
Hornak V, Simmerling C (2003) Generation of accurate protein loop conformations through low-barrier molecular dynamics. Proteins 51(4):577-590. (Pubitemid 36676142)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.51
, Issue.4
, pp. 577-590
-
-
Hornak, V.1
Simmerling, C.2
-
84
-
-
80052027212
-
Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations
-
Olson MA, Chaudhury S, Lee MS (2011) Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations. J. Comp. Chem. 32(14):3014-3022.
-
(2011)
J. Comp. Chem
, vol.32
, Issue.14
, pp. 3014-3022
-
-
Olson, M.A.1
Chaudhury, S.2
Lee, M.S.3
-
86
-
-
33645344484
-
The genetic algorithm approach to protein structure prediction
-
Unger R (2004) The genetic algorithm approach to protein structure prediction, Structure and Bonding 110:153-175.
-
(2004)
Structure and Bonding
, vol.110
, pp. 153-175
-
-
Unger, R.1
-
87
-
-
84863775602
-
Refinement of protein structure homology models via long, all-atom molecular dynamics simualtions
-
Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE (2012) Refinement of protein structure homology models via long, all-atom molecular dynamics simualtions. Proteins 80:2071-2079.
-
(2012)
Proteins
, vol.80
, pp. 2071-2079
-
-
Raval, A.1
Piana, S.2
Eastwood, M.P.3
Dror, R.O.4
Shaw, D.E.5
-
88
-
-
0034237227
-
A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins
-
DOI 10.1002/(SICI)1097-0134(20000701)40:1<135: :AID-PROT150>3.0. CO;2-1
-
Deane CM, Blundell TL (2000) A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins. Proteins 40(1):135-144. (Pubitemid 30368589)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.40
, Issue.1
, pp. 135-144
-
-
Deane, C.M.1
Blundell, T.L.2
|