-
1
-
-
70350774312
-
Protein structure prediction based on sequence similarity
-
Jaroszewski, L. (2009) Protein structure prediction based on sequence similarity, Methods Mol Biol 569, 129-156.
-
(2009)
Methods Mol Biol
, vol.569
, pp. 129-156
-
-
Jaroszewski, L.1
-
2
-
-
0022788691
-
An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
-
Moult, J., and James, M. N. (1986) An algorithm for determining the conformation of polypeptide segments in proteins by systematic search, Proteins 1, 146-163.
-
(1986)
Proteins
, vol.1
, pp. 146-163
-
-
Moult, J.1
James, M.N.2
-
3
-
-
0034665713
-
Structural mechanism for STI-571 inhibition of abelson tyrosine kinase
-
Schindler, T., Bornmann, W., Pellicena, P., Miller, W. T., Clarkson, B., and Kuriyan, J. (2000) Structural mechanism for STI-571 inhibition of abelson tyrosine kinase, Science 289, 1938-1942.
-
(2000)
Science
, vol.289
, pp. 1938-1942
-
-
Schindler, T.1
Bornmann, W.2
Pellicena, P.3
Miller, W.T.4
Clarkson, B.5
Kuriyan, J.6
-
4
-
-
58149102648
-
Type-II kinase inhibitor docking screening, and profi ling using modifi ed structures of active kinase states
-
Kufareva, I., and Abagyan, R. (2008) Type-II kinase inhibitor docking, screening, and profi ling using modifi ed structures of active kinase states, J Med Chem 51, 7921-7932.
-
(2008)
J Med Chem
, vol.51
, pp. 7921-7932
-
-
Kufareva, I.1
Abagyan, R.2
-
5
-
-
0033954256
-
The protein data bank
-
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank, Nucleic acids research 28, 235-242. (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
6
-
-
0028066936
-
Comparison of systematic search and database methods for constructing segments of protein structure
-
Fidelis, K., Stern, P. S., Bacon, D., and Moult, J. (1994) Comparison of systematic search and database methods for constructing segments of protein structure, Protein Eng 7, 953-960. (Pubitemid 24256873)
-
(1994)
Protein Engineering
, vol.7
, Issue.8
, pp. 953-960
-
-
Fidelis, K.1
Stern, P.S.2
Bacon, D.3
Moult, J.4
-
7
-
-
0035107308
-
CODA: A combined algorithm for predicting the structurally variable regions of protein models
-
DOI 10.1110/ps.37601
-
Deane, C. M., and Blundell, T. L. (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
-
8
-
-
0031564640
-
PDB-based protein loop prediction: Parameters for selection and methods for optimization
-
DOI 10.1006/jmbi.1996.0857
-
van Vlijmen, H. W., and Karplus, M. (1997) PDB-based protein loop prediction: parameters for selection and methods for optimization, J Mol Biol 267, 975-1001. (Pubitemid 27192667)
-
(1997)
Journal of Molecular Biology
, vol.267
, Issue.4
, pp. 975-1001
-
-
Van Vlijmen, H.W.T.1
Karplus, M.2
-
9
-
-
0033603394
-
New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification
-
DOI 10.1006/jmbi.1999.2826
-
Wojcik, J., Mornon, J. P., and Chomilier, J. (1999) New effi cient statistical sequencedependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classifi cation, J Mol Biol 289, 1469-1490. (Pubitemid 29296718)
-
(1999)
Journal of Molecular Biology
, vol.289
, Issue.5
, pp. 1469-1490
-
-
Wojcik, J.1
Mornon, J.-P.2
Chomilier, J.3
-
10
-
-
1442310610
-
Loops In Proteins (LIP) - A comprehensive loop database for homology modelling
-
Michalsky, E., Goede, A., and Preissner, R. (2003) Loops In Proteins (LIP)-a comprehensive loop database for homology modelling, Protein Eng 16, 979-985. (Pubitemid 38281748)
-
(2003)
Protein Engineering
, vol.16
, Issue.12
, pp. 979-985
-
-
Michalsky, E.1
Goede, A.2
Preissner, R.3
-
11
-
-
0034847744
-
Improved protein loop prediction from sequence alone
-
Burke, D. F., and Deane, C. M. (2001) Improved protein loop prediction from sequence alone, Protein Eng 14, 473-478. (Pubitemid 32846932)
-
(2001)
Protein Engineering
, vol.14
, Issue.7
, pp. 473-478
-
-
Burke, D.F.1
Deane, C.M.2
-
12
-
-
33748959731
-
Saturating representation of loop conformational fragments in structure databanks
-
Fernandez-Fuentes, N., and Fiser, A. (2006) Saturating representation of loop conformational fragments in structure databanks, BMC Struct Biol 6, 15.
-
(2006)
BMC Struct Biol
, vol.6
, pp. 15
-
-
Fernandez-Fuentes, N.1
Fiser, A.2
-
13
-
-
77949561118
-
Mining protein loops using a structural alphabet and statistical exceptionality
-
Regad, L., Martin, J., Nuel, G., and Camproux, A. C. (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.C.4
-
14
-
-
77951229808
-
FREAD revisited: Accurate loop structure prediction using a database search algorithm
-
Choi, Y., and Deane, C. M. (2010) FREAD revisited: Accurate loop structure prediction using a database search algorithm, Proteins 78, 1431-1440.
-
(2010)
Proteins
, vol.78
, pp. 1431-1440
-
-
Choi, Y.1
Deane, C.M.2
-
15
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
DOI 10.1006/jmbi.1997.0959
-
Simons, K. T., Kooperberg, C., Huang, E., and Baker, D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions, J Mol Biol 268, 209-225. (Pubitemid 27192690)
-
(1997)
Journal of Molecular Biology
, vol.268
, Issue.1
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
16
-
-
2442449534
-
Modeling structurally variable regions in homologous proteins with rosetta
-
DOI 10.1002/prot.10629
-
Rohl, C. A., Strauss, C. E., Chivian, D., and 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
-
17
-
-
68349104348
-
Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
-
Mandell, D. J., Coutsias, E. A., and 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
-
18
-
-
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, C. M., and Blundell, T. L. (2000) A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins, Proteins 40, 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
-
19
-
-
0036096608
-
A divide and conquer approach to fast loop modeling
-
Tosatto, S. C., Bindewald, E., Hesser, J., and Manner, R. (2002) A divide and conquer approach to fast loop modeling, Protein Eng 15, 279-286. (Pubitemid 34532766)
-
(2002)
Protein Engineering
, vol.15
, Issue.4
, pp. 279-286
-
-
Tosatto, S.C.E.1
Bindewald, E.2
Hesser, J.3
Manner, R.4
-
20
-
-
39749085824
-
LOOPER: A molecular mechanics-based algorithm for protein loop prediction
-
DOI 10.1093/protein/gzm083
-
Spassov, V. Z., Flook, P. K., and Yan, L. (2008) LOOPER: a molecular mechanics-based algorithm for protein loop prediction, Protein Eng Des Sel 21, 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
-
21
-
-
0034870539
-
Ab initio modeling of small
-
Galaktionov, S., Nikiforovich, G. V., and Marshall, G. R. (2001) Ab initio modeling of small, medium, and large loops in proteins, Biopolymers 60, 153-168.
-
(2001)
Medium, and Large Loops in Proteins, Biopolymers
, vol.60
, pp. 153-168
-
-
Galaktionov, S.1
Nikiforovich, G.V.2
Marshall, G.R.3
-
22
-
-
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, C. S., and Friesner, R. A. (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
-
23
-
-
0031855094
-
Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model
-
DOI 10.1002/(SICI)1097-0134(19980901)32:4<475::AID-PROT6>3.0.CO;2-F
-
Kolinski, A., and Skolnick, J. (1998) Assembly of protein structure from sparse experimental data: an effi cient Monte Carlo model, Proteins 32, 475-494. (Pubitemid 28380787)
-
(1998)
Proteins: Structure, Function and Genetics
, vol.32
, Issue.4
, pp. 475-494
-
-
Kolinski, A.1
Skolnick, J.2
-
24
-
-
40549088876
-
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions
-
DOI 10.1002/jcc.20827
-
Olson, M. A., Feig, M., and Brooks, C. L., 3rd. (2008) Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions, J Comput Chem 29, 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
-
25
-
-
0002336164
-
Ring closure and local conformational deformations of chain molecules
-
Go, N., and Scheraga, H. A. (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.A.2
-
26
-
-
0000781576
-
Exact analytical loop closure in proteins using polynomial equations
-
Wedemeyer, W. J., and Scheraga, H. A. (1999) Exact analytical loop closure in proteins using polynomial equations, Journal of Computational Chemistry 20, 819-844. (Pubitemid 129656130)
-
(1999)
Journal of Computational Chemistry
, vol.20
, Issue.8
, pp. 819-844
-
-
Wedemeyer, W.J.1
Scheraga, H.A.2
-
27
-
-
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., and Koehl, P. (2005) Inverse Kinematics in Biology: The Protein Loop Closure Problem., Int J Robotics Research 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
-
28
-
-
1442281405
-
A kinematic view of loop closure
-
Coutsias, E. A., Seok, C., Jacobson, M. P., and Dill, K. A. (2004) A kinematic view of loop closure, J Comput Chem 25, 510-528.
-
(2004)
J Comput Chem
, vol.25
, pp. 510-528
-
-
Coutsias, E.A.1
Seok, C.2
Jacobson, M.P.3
Dill, K.A.4
-
29
-
-
79955906529
-
Assessing protein loop flexibility by hierarchical monte carlo sampling
-
Nilmeier, J., Hua, L., Coutsias, E. A., and Jacobson, M. P. (2011) Assessing Protein Loop Flexibility by Hierarchical Monte Carlo Sampling, Journal of Chemical Theory and Computation 7, 1564-1574.
-
(2011)
Journal of Chemical Theory and Computation
, vol.7
, pp. 1564-1574
-
-
Nilmeier, J.1
Hua, L.2
Coutsias, E.A.3
Jacobson, M.P.4
-
30
-
-
56549099908
-
Prediction of protein loop structures using a local move Monte Carlo approach and a gridbased force fi eld
-
Cui, M., Mezei, M., and Osman, R. (2008) Prediction of protein loop structures using a local move Monte Carlo approach and a gridbased force fi eld, Protein Eng Des Sel 21, 729-735.
-
(2008)
Protein Eng des Sel
, vol.21
, pp. 729-735
-
-
Cui, M.1
Mezei, M.2
Osman, R.3
-
31
-
-
73649194755
-
Stereochemistry of polypeptide chain confi gurations
-
Ramachandran, G. N., Ramakrishnan, C., and Sasisekharan, V. (1963) Stereochemistry of polypeptide chain confi gurations, J Mol Biol 7, 95-99.
-
(1963)
J Mol Biol
, vol.7
, pp. 95-99
-
-
Ramachandran, G.N.1
Ramakrishnan, C.2
Sasisekharan, V.3
-
32
-
-
0037406075
-
Cyclic coordinate descent: A robotics algorithm for protein loop closure
-
DOI 10.1110/ps.0242703
-
Canutescu, A. A., and Dunbrack, R. L., Jr. (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
-
33
-
-
70349758444
-
Conformation dependence of backbone geometry in proteins
-
Berkholz, D. S., Shapovalov, M. V., Dunbrack, R. L., Jr., and Karplus, P. A. (2009) Conformation dependence of backbone geometry in proteins, Structure 17, 1316-1325.
-
(2009)
Structure
, vol.17
, pp. 1316-1325
-
-
Berkholz, D.S.1
Shapovalov, M.V.2
Dunbrack Jr., R.L.3
Karplus, P.A.4
-
34
-
-
58149212059
-
Predictions of protein backbone bond distances and angles from fi rst principles
-
Schaefer, L., and Cao, M. (1995) Predictions of protein backbone bond distances and angles from fi rst principles, Journal of Molecular Structure: THEOCHEM 333, 201-208.
-
(1995)
Journal of Molecular Structure: THEOCHEM
, vol.333
, pp. 201-208
-
-
Schaefer, L.1
Cao, M.2
-
35
-
-
0030010605
-
Experimentally observed conformation-dependent geometry and hidden strain in proteins
-
Karplus, P. A. (1996) Experimentally observed conformation-dependent geometry and hidden strain in proteins, Protein Sci 5, 1406-1420. (Pubitemid 26239448)
-
(1996)
Protein Science
, vol.5
, Issue.7
, pp. 1406-1420
-
-
Karplus, P.A.1
-
36
-
-
0001720782
-
Chain closure with bond angle variations
-
Bruccoleri, R. E., and Karplus, M. (1985) Chain closure with bond angle variations, Macromolecules 18, 2767-2773.
-
(1985)
Macromolecules
, vol.18
, pp. 2767-2773
-
-
Bruccoleri, R.E.1
Karplus, M.2
-
37
-
-
25444455574
-
Full cyclic coordinate descent: Solving the protein loop closure problem in Calpha space
-
Boomsma, W., and Hamelryck, T. (2005) Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space, BMC bioinformatics 6, 159.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 159
-
-
Boomsma, W.1
Hamelryck, T.2
-
38
-
-
33748988479
-
Long loop prediction using the protein local optimization program
-
DOI 10.1002/prot.21040
-
Zhu, K., Pincus, D. L., Zhao, S., and Friesner, R. A. (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
-
39
-
-
1842532008
-
A hierarchical approach to all-atom protein loop prediction
-
DOI 10.1002/prot.10613
-
Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J., Honig, B., Shaw, D. E., and Friesner, R. A. (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
-
40
-
-
0023478807
-
Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures
-
Shenkin, P. S., Yarmush, D. L., Fine, R. M., Wang, H. J., and Levinthal, C. (1987) Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures, Biopolymers 26, 2053-2085.
-
(1987)
Biopolymers
, vol.26
, pp. 2053-2085
-
-
Shenkin, P.S.1
Yarmush, D.L.2
Fine, R.M.3
Wang, H.J.4
Levinthal, C.5
-
41
-
-
0037188507
-
Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction
-
DOI 10.1073/pnas.102179699
-
Xiang, Z., Soto, C. S., and Honig, B. (2002) Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction, Proc Natl Acad Sci U S A 99, 7432-7437. (Pubitemid 34568708)
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.11
, pp. 7432-7437
-
-
Xiang, Z.1
Soto, C.S.2
Honig, B.3
-
42
-
-
0027164958
-
Determining protein loop conformation using scaling-relaxation techniques
-
Zheng, Q., Rosenfeld, R., Vajda, S., and DeLisi, C. (1993) Determining protein loop conformation using scaling-relaxation techniques, Protein Sci 2, 1242-1248. (Pubitemid 23225647)
-
(1993)
Protein Science
, vol.2
, Issue.8
, pp. 1242-1248
-
-
Zheng, Q.1
Rosenfeld, R.2
Vajda, S.3
DeLisi, C.4
-
43
-
-
0037375742
-
Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles
-
DOI 10.1002/prot.10285
-
DePristo, M. A., de Bakker, P. I., Lovell, S. C., and Blundell, T. L. (2003) Ab initio construction of polypeptide fragments: effi cient generation of accurate, representative ensembles, Proteins 51, 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
-
44
-
-
0029063717
-
The complexity and accuracy of discrete state models of protein structure
-
Park, B. H., and Levitt, M. (1995) The complexity and accuracy of discrete state models of protein structure, J Mol Biol 249, 493-507.
-
(1995)
J Mol Biol
, vol.249
, pp. 493-507
-
-
Park, B.H.1
Levitt, M.2
-
45
-
-
0026009212
-
Prediction of protein backbone conformation based on seven structure assignments: Influence of local interactions
-
Rooman, M. J., Kocher, J. P., and Wodak, S. J. (1991) Prediction of protein backbone conformation based on seven structure assignments. Infl uence of local interactions, J Mol Biol 221, 961-979. (Pubitemid 121003430)
-
(1991)
Journal of Molecular Biology
, vol.221
, Issue.3
, pp. 961-979
-
-
Rooman, M.J.1
Kocher, J.-P.A.2
Wodak, S.J.3
-
46
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser, A., Do, R. K., and 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.2
Sali, A.3
-
47
-
-
70049088996
-
A self-organizing algorithm for modeling protein loops
-
Liu, P., Zhu, F., Rassokhin, D. N., and Agrafi otis, D. K. (2009) A self-organizing algorithm for modeling protein loops, PLoS Comput Biol 5, e1000478.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Liu, P.1
Zhu, F.2
Rassokhin, D.N.3
Agrafi Otis, D.K.4
-
48
-
-
0033198024
-
Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR data
-
DOI 10.1002/(SICI)1097-0282(199909)50:3<329::AID-BIP8>3.0.CO;2-4
-
Baysal, C., and Meirovitch, H. (1999) Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR data, Biopolymers 50, 329-344. (Pubitemid 29334307)
-
(1999)
Biopolymers
, vol.50
, Issue.3
, pp. 329-344
-
-
Baysal, C.1
Meirovitch, H.2
-
49
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
Scott, W. R. P., Hünenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Krüger, P., and van Gunsteren, W. F. (1999) The GROMOS Biomolecular Simulation Program Package, The Journal of Physical Chemistry A 103, 3596-3607. (Pubitemid 129570863)
-
(1999)
Journal of Physical Chemistry A
, vol.103
, Issue.19
, pp. 3596-3607
-
-
Scott, W.R.P.1
Hunenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Kruger, P.9
Van Gunsteren, W.F.10
-
50
-
-
0031021792
-
A fast and effi cient program for modeling protein loops
-
Zhang, H., Lai, L., Wang, L., Han, Y., and Tang, Y. (1997) A fast and effi cient program for modeling protein loops, Biopolymers 41, 61-72.
-
(1997)
Biopolymers
, vol.41
, pp. 61-72
-
-
Zhang, H.1
Lai, L.2
Wang, L.3
Han, Y.4
Tang, Y.5
-
51
-
-
0242443693
-
Force fi elds for protein simulations
-
Ponder, J. W., and Case, D. A. (2003) Force fi elds for protein simulations, Adv Protein Chem 66, 27-85.
-
(2003)
Adv Protein Chem
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
52
-
-
0033654297
-
Generalized born models of macromolecular solvation effects
-
Bashford, D., and Case, D. A. (2000) Generalized born models of macromolecular solvation effects, Annu Rev Phys Chem 51, 129-152.
-
(2000)
Annu Rev Phys Chem
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.A.2
-
53
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
DOI 10.1006/jmbi.1997.1479
-
Samudrala, R., and Moult, J. (1998) An allatom distance-dependent conditional probability discriminatory function for protein structure prediction, J Mol Biol 275, 895-916. (Pubitemid 28077703)
-
(1998)
Journal of Molecular Biology
, vol.275
, Issue.5
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
54
-
-
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., DePristo, M. A., Burke, D. F., and Blundell, T. L. (2003) Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force fi eld 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
-
55
-
-
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., and Zhou, Y. (2002) Distancescaled, fi nite 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
-
56
-
-
1642575364
-
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential
-
DOI 10.1110/ps.03411904
-
Zhang, C., Liu, S., and Zhou, Y. (2004) Accurate and effi cient loop selections by the DFIRE-based all-atom statistical potential, Protein Sci 13, 391-399. (Pubitemid 38124960)
-
(2004)
Protein Science
, vol.13
, Issue.2
, pp. 391-399
-
-
Zhang, C.1
Liu, S.2
Zhou, Y.3
-
57
-
-
77951215074
-
New computational method for prediction of interacting protein loop regions
-
Danielson, M. L., and Lill, M. A. (2010) New computational method for prediction of interacting protein loop regions, Proteins 78, 1748-1759.
-
(2010)
Proteins
, vol.78
, pp. 1748-1759
-
-
Danielson, M.L.1
Lill, M.A.2
-
58
-
-
77149152176
-
Backbone statistical potential from local sequence-structure interactions in protein loops
-
Rata, I. A., Li, Y., and Jakobsson, E. (2010) Backbone statistical potential from local sequence-structure interactions in protein loops, J Phys Chem B 114, 1859-1869.
-
(2010)
J Phys Chem B
, vol.114
, pp. 1859-1869
-
-
Rata, I.A.1
Li, Y.2
Jakobsson, E.3
-
59
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
DOI 10.1006/jmbi.1993.1626
-
Sali, A., and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints, J Mol Biol 234, 779-815. (Pubitemid 24007801)
-
(1993)
Journal of Molecular Biology
, vol.234
, Issue.3
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
60
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Bashford, D., Bellott, Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiórkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, The Journal of Physical Chemistry B 102, 3586-3616. (Pubitemid 128576688)
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
61
-
-
0031582083
-
Novel knowledge-based mean force potential at atomic
-
DOI 10.1006/jmbi.1996.0868
-
Melo, F., and Feytmans, E. (1997) Novel knowledge-based mean force potential at atomic level, J Mol Biol 267, 207-222. (Pubitemid 27149749)
-
(1997)
Journal of Molecular Biology
, vol.267
, Issue.1
, pp. 207-222
-
-
Melo, F.1
Feytmans, E.2
-
62
-
-
0023155210
-
Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
DOI 10.1016/0022-2836(87)90358-5
-
Ponder, J. W., and Richards, F. M. (1987) Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes, J Mol Biol 193, 775-791. (Pubitemid 17020078)
-
(1987)
Journal of Molecular Biology
, vol.193
, Issue.4
, pp. 775-791
-
-
Ponder, J.W.1
Richards, F.M.2
-
63
-
-
47349128896
-
Toward better refinement of comparative models: Predicting loops in inexact environments
-
DOI 10.1002/prot.21990
-
Sellers, B. D., Zhu, K., Zhao, S., Friesner, R. A., and Jacobson, M. P. (2008) Toward better refi nement of comparative models: predicting loops in inexact environments, Proteins 72, 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
-
64
-
-
38549154569
-
Loop modeling: Sampling
-
Soto, C. S., Fasnacht, M., Zhu, J., Forrest, L., and Honig, B. (2008) Loop modeling: Sampling, fi ltering, and scoring, Proteins 70, 834-843.
-
(2008)
Fi Ltering, and Scoring, Proteins
, vol.70
, pp. 834-843
-
-
Soto, C.S.1
Fasnacht, M.2
Zhu, J.3
Forrest, L.4
Honig, B.5
-
65
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
DOI 10.1021/jp003919d
-
Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., and Jorgensen, W. L. (2001) Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides, The Journal of Physical Chemistry B 105, 6474-6487. (Pubitemid 35339015)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.28
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
66
-
-
0000374885
-
-
Advances in Physical Organic Chemistry, Academic Press
-
Scheraga, H. A., and Gold, V. (1968) Calculations of Conformations of Polypeptides, in Advances in Physical Organic Chemistry, pp 103-184, Academic Press.
-
(1968)
Calculations of Conformations of Polypeptides
, pp. 103-184
-
-
Scheraga, H.A.1
Gold, V.2
-
67
-
-
0001731773
-
Energy parameters in polypeptides.10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm with application to praline-containing peptides
-
Némethy, G., Gibson, K. D., Palmer, K. A., Yoon, C. N., Paterlini, G., Zagari, A., Rumsey, S., and Scheraga, H. A. (1992) Energy parameters in polypeptides.10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to praline-containing peptides Journal of physical chemistry 96, 6472.
-
(1992)
Journal of Physical Chemistry
, vol.96
, pp. 6472
-
-
Némethy, G.1
Gibson, K.D.2
Palmer, K.A.3
Yoon, C.N.4
Paterlini, G.5
Zagari, A.6
Rumsey, S.7
Scheraga, H.A.8
-
68
-
-
58149157667
-
Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling
-
Felts, A. K., Gallicchio, E., Chekmarev, D., Paris, K. A., Friesner, R. A., and Levy, R. M. (2008) Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling, J Chem Theory Comput 4, 855-868.
-
(2008)
J Chem Theory Comput
, vol.4
, 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
-
69
-
-
0024084758
-
A rapid method of calculating charge-charge interaction energies in proteins
-
Pickersgill, R. W. (1988) A rapid method of calculating charge-charge interaction energies in proteins, Protein Eng 2, 247-248.
-
(1988)
Protein Eng
, vol.2
, pp. 247-248
-
-
Pickersgill, R.W.1
-
70
-
-
0042208326
-
On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy
-
DOI 10.1021/ja029833a
-
Levy, R. M., Zhang, L. Y., Gallicchio, E., and Felts, A. K. (2003) On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute-Solvent Interaction Energy, Journal of the American Chemical Society 125, 9523-9530. (Pubitemid 36936069)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.31
, pp. 9523-9530
-
-
Levy, R.M.1
Zhang, L.Y.2
Gallicchio, E.3
Felts, A.K.4
-
71
-
-
1442330396
-
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
-
Gallicchio, E., and Levy, R. M. (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
-
72
-
-
0035874147
-
Optimization of solvation models for predicting the structure of surface loops in proteins
-
DOI 10.1002/prot.1041
-
Das, B., and Meirovitch, H. (2001) Optimization of solvation models for predicting the structure of surface loops in proteins, Proteins 43, 303-314. (Pubitemid 32367805)
-
(2001)
Proteins: Structure, Function and Genetics
, vol.43
, Issue.3
, pp. 303-314
-
-
Das, B.1
Meirovitch, H.2
-
73
-
-
0038300292
-
Solvation parameters for predicting the structure of surface loops in proteins: Transferability and entropic effects
-
DOI 10.1002/prot.10356
-
Das, B., and Meirovitch, H. (2003) Solvation parameters for predicting the structure of surface loops in proteins: transferability and entropic effects, Proteins 51, 470-483. (Pubitemid 36528831)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.51
, Issue.3
, pp. 470-483
-
-
Das, B.1
Meirovitch, H.2
-
74
-
-
33644787382
-
Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins
-
DOI 10.1021/jp055771+
-
Szarecka, A., and Meirovitch, H. (2006) Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins, J Phys Chem B 110, 2869-2880. (Pubitemid 43342883)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.6
, pp. 2869-2880
-
-
Szarecka, A.1
Meirovitch, H.2
-
75
-
-
0027080909
-
Atomic solvation parameters applied to molecular dynamics of proteins in solution
-
Wesson, L., and Eisenberg, D. (1992) Atomic solvation parameters applied to molecular dynamics of proteins in solution, Protein Sci 1, 227-235. (Pubitemid 23007289)
-
(1992)
Protein Science
, vol.1
, Issue.2
, pp. 227-235
-
-
Wesson, L.1
Eisenberg, D.2
-
76
-
-
78650798307
-
Development of a new physicsbased internal coordinate mechanics force fi eld and its application to protein loop modeling
-
Arnautova, Y. A., Abagyan, R. A., and Totrov, M. (2011) Development of a new physicsbased internal coordinate mechanics force fi eld and its application to protein loop modeling, Proteins 79, 477-498.
-
(2011)
Proteins
, vol.79
, pp. 477-498
-
-
Arnautova, Y.A.1
Abagyan, R.A.2
Totrov, M.3
-
77
-
-
84986522918
-
ICM-A new method for protein modeling and design: Applications to
-
Abagyan, R., Totrov, M., and Kuznetsov, D. (1994) ICM-A new method for protein modeling and design: Applications to J Comp Chem 15, 488-506.
-
(1994)
J Comp Chem
, vol.15
, pp. 488-506
-
-
Abagyan, R.1
Totrov, M.2
Kuznetsov, D.3
-
78
-
-
0027955787
-
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
-
DOI 10.1006/jmbi.1994.1052
-
Abagyan, R., and Totrov, M. (1994) Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins, J Mol Biol 235, 983-1002. (Pubitemid 24047836)
-
(1994)
Journal of Molecular Biology
, vol.235
, Issue.3
, pp. 983-1002
-
-
Abagyan, R.1
Totrov, M.2
-
79
-
-
30344475200
-
Progress over the first decade of CASP experiments
-
DOI 10.1002/prot.20740
-
Kryshtafovych, A., Venclovas, C., Fidelis, K., and Moult, J. (2005) Progress over the fi rst decade of CASP experiments, Proteins 61 Suppl 7, 225-236. (Pubitemid 43069977)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.61
, Issue.SUPPL. 7
, pp. 225-236
-
-
Kryshtafovych, A.1
Venclovas, C.2
Fidelis, K.3
Moult, J.4
-
80
-
-
77449146970
-
Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors
-
Nikiforovich, G. V., Taylor, C. M., Marshall, G. R., and Baranski, T. J. (2010) Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors, Proteins 78, 271-285.
-
(2010)
Proteins
, vol.78
, pp. 271-285
-
-
Nikiforovich, G.V.1
Taylor, C.M.2
Marshall, G.R.3
Baranski, T.J.4
-
81
-
-
77955796067
-
Antibodies as a model system for comparative model refi nement
-
Sellers, B. D., Nilmeier, J. P., and Jacobson, M. P. (2010) Antibodies as a model system for comparative model refi nement, Proteins 78, 2490-2505.
-
(2010)
Proteins
, vol.78
, pp. 2490-2505
-
-
Sellers, B.D.1
Nilmeier, J.P.2
Jacobson, M.P.3
-
82
-
-
0033056708
-
Folding funnels, binding funnels, and protein function
-
Tsai, C. J., Kumar, S., Ma, B., and Nussinov, R. (1999) Folding funnels, binding funnels, and protein function, Protein Sci 8, 1181-1190. (Pubitemid 29264948)
-
(1999)
Protein Science
, vol.8
, Issue.6
, pp. 1181-1190
-
-
Tsai, C.-J.1
Kumar, S.2
Ma, B.3
Nussinov, R.4
-
83
-
-
40549107133
-
Conformational selection in silico: Loop latching motions and ligand binding in enzymes
-
DOI 10.1002/prot.21666
-
Wong, S., and Jacobson, M. P. (2008) Conformational selection in silico: loop latching motions and ligand binding in enzymes, Proteins 71, 153-164. (Pubitemid 351358599)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.71
, Issue.1
, pp. 153-164
-
-
Wong, S.1
Jacobson, M.P.2
-
84
-
-
33747863016
-
ArchPRED: A template based loop structure prediction server
-
DOI 10.1093/nar/gkl113
-
Fernandez-Fuentes, N., Zhai, J., and Fiser, A. (2006) ArchPRED: a template based loop structure prediction server, Nucleic acids research 34, W173-176. (Pubitemid 44529758)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.WEB. SERV. ISS.
-
-
Fernandez-Fuentes, N.1
Zhai, J.2
Fiser, A.3
-
85
-
-
0346882663
-
ModLoop: Automated modeling of loops in protein structures
-
DOI 10.1093/bioinformatics/btg362
-
Fiser, A., and Sali, A. (2003) ModLoop: automated modeling of loops in protein structures, Bioinformatics (Oxford, England) 19, 2500-2501. (Pubitemid 38016660)
-
(2003)
Bioinformatics
, vol.19
, Issue.18
, pp. 2500-2501
-
-
Fiser, A.1
Sali, A.2
-
86
-
-
23144443837
-
RPBS: A web resource for structural bioinformatics
-
DOI 10.1093/nar/gki477
-
Alland, C., Moreews, F., Boens, D., Carpentier, M., Chiusa, S., Lonquety, M., Renault, N., Wong, Y., Cantalloube, H., Chomilier, J., Hochez, J., Pothier, J., Villoutreix, B. O., Zagury, J. F., and Tuffery, P. (2005) RPBS: a web resource for structural bioinformatics, Nucleic acids research 33, W44-49. (Pubitemid 44529878)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Alland, C.1
Moreews, F.2
Boens, D.3
Carpentier, M.4
Chiusa, S.5
Lonquety, M.6
Renault, N.7
Wong, Y.8
Cantalloube, H.9
Chomilier, J.10
Hochez, J.11
Pothier, J.12
Villoutreix, B.O.13
Zagury, J.-F.14
Tuffery, P.15
|