-
1
-
-
17244367767
-
Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis
-
Mooney S, (2005) Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. Brief Bioinform 6: 44-56.
-
(2005)
Brief Bioinform
, vol.6
, pp. 44-56
-
-
Mooney, S.1
-
2
-
-
0032991552
-
Characterization of single-nucleotide polymorphisms in coding regions of human genes
-
Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 22: 231-238.
-
(1999)
Nat Genet
, vol.22
, pp. 231-238
-
-
Cargill, M.1
Altshuler, D.2
Ireland, J.3
Sklar, P.4
Ardlie, K.5
-
3
-
-
0032990407
-
Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis
-
Halushka MK, Fan JB, Bentley K, Hsie L, Shen N, et al. (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet 22: 239-247.
-
(1999)
Nat Genet
, vol.22
, pp. 239-247
-
-
Halushka, M.K.1
Fan, J.B.2
Bentley, K.3
Hsie, L.4
Shen, N.5
-
4
-
-
0036321534
-
Assessing the relative importance of the biophysical properties of amino acid substitutions associated with human genetic disease
-
Terp BN, Cooper DN, Christensen IT, Jørgensen FS, Bross P, et al. (2002) Assessing the relative importance of the biophysical properties of amino acid substitutions associated with human genetic disease. Human Mutat 20: 98-109.
-
(2002)
Human Mutat
, vol.20
, pp. 98-109
-
-
Terp, B.N.1
Cooper, D.N.2
Christensen, I.T.3
Jørgensen, F.S.4
Bross, P.5
-
5
-
-
1542577828
-
The amino-acid mutational spectrum of human genetic disease
-
Vitkup D, Sander C, Church GM, (2003) The amino-acid mutational spectrum of human genetic disease. Genome Biol 4: R72.
-
(2003)
Genome Biol
, vol.4
-
-
Vitkup, D.1
Sander, C.2
Church, G.M.3
-
6
-
-
0036300807
-
Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties
-
Ferrer-Costa C, Orozco M, de la Cruz X, (2002) Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties. J Mol Biol 315: 771-786.
-
(2002)
J Mol Biol
, vol.315
, pp. 771-786
-
-
Ferrer-Costa, C.1
Orozco, M.2
de la Cruz, X.3
-
7
-
-
0037432532
-
Structural location of disease-associated single-nucleotide polymorphisms
-
Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, et al. (2003) Structural location of disease-associated single-nucleotide polymorphisms. J Mol Biol 327: 1021-1030.
-
(2003)
J Mol Biol
, vol.327
, pp. 1021-1030
-
-
Stitziel, N.O.1
Tseng, Y.Y.2
Pervouchine, D.3
Goddeau, D.4
Kasif, S.5
-
8
-
-
0141833160
-
The functional importance of disease-associated mutation
-
Mooney SD, Klein TE, (2002) The functional importance of disease-associated mutation. BMC Bioinformatics 3: 24.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 24
-
-
Mooney, S.D.1
Klein, T.E.2
-
9
-
-
0036387236
-
Evaluation of structural and evolutionary contributions to deleterious mutation prediction
-
Saunders CT, Baker D, (2002) Evaluation of structural and evolutionary contributions to deleterious mutation prediction. J Mol Biol Vol. 322: 891-901.
-
(2002)
J Mol Biol
, vol.322
, pp. 891-901
-
-
Saunders, C.T.1
Baker, D.2
-
10
-
-
0344033683
-
A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function
-
Krishnan VG, Westhead DR, (2003) A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function. Bioinformatics 19: 2199-2209.
-
(2003)
Bioinformatics
, vol.19
, pp. 2199-2209
-
-
Krishnan, V.G.1
Westhead, D.R.2
-
11
-
-
79959449643
-
Studies on adaptability of binding residues and flap region of TMC-114 resistance HIV-1 protease mutants
-
Purohit R, Rajendran V, Sethumadhavan R, (2011) Studies on adaptability of binding residues and flap region of TMC-114 resistance HIV-1 protease mutants. Journal of Biomolecular Structure & Dynamics 29(1): 137-152.
-
(2011)
Journal of Biomolecular Structure & Dynamics
, vol.29
, Issue.1
, pp. 137-152
-
-
Purohit, R.1
Rajendran, V.2
Sethumadhavan, R.3
-
12
-
-
84899920528
-
Role of ELA region in auto-activation of mutant KIT receptor; a molecular dynamics simulation insight
-
[epub ahead of print]. DOI 10.1080/07391102.2013.803264
-
Purohit R. (2013). Role of ELA region in auto-activation of mutant KIT receptor; a molecular dynamics simulation insight. J Biomol Struct Dyn [epub ahead of print]. DOI:10.1080/07391102.2013.803264.
-
(2013)
J Biomol Struct Dyn
-
-
Purohit, R.1
-
13
-
-
84889685004
-
Drug resistance mechanism of PncA in Mycobacterium tuberculosis
-
Rajendran V, Sethumadhavan R, (2014) Drug resistance mechanism of PncA in Mycobacterium tuberculosis. J Biomol Struct Dyn 32(2): 209-21.
-
(2014)
J Biomol Struct Dyn
, vol.32
, Issue.2
, pp. 209-221
-
-
Rajendran, V.1
Sethumadhavan, R.2
-
14
-
-
84864771186
-
In silico investigation of molecular mechanism of laminopathy caused by a point mutation (R482W) in lamin A/C protein
-
Rajendran V, Purohit R, Sethumadhavan R, (2012) In silico investigation of molecular mechanism of laminopathy caused by a point mutation (R482W) in lamin A/C protein. Amino Acids 43(2): 603-15.
-
(2012)
Amino Acids
, vol.43
, Issue.2
, pp. 603-615
-
-
Rajendran, V.1
Purohit, R.2
Sethumadhavan, R.3
-
15
-
-
84872270918
-
Computational screening and molecular dynamics simulation of disease associated nsSNPs in CENP-E
-
Kumar A, Purohit R, (2012) Computational screening and molecular dynamics simulation of disease associated nsSNPs in CENP-E. Mut Res 738-739: 28-37.
-
(2012)
Mut Res
, vol.738-739
, pp. 28-37
-
-
Kumar, A.1
Purohit, R.2
-
16
-
-
84888365817
-
Evidence of Colorectal Cancer-Associated Mutation in MCAK: A Computational Report
-
Kumar A, Rajendran V, Sethumadhavan R, Purohit R, (2013) Evidence of Colorectal Cancer-Associated Mutation in MCAK: A Computational Report. Cell Biochem Biophys 67(3): 837-51.
-
(2013)
Cell Biochem Biophys
, vol.67
, Issue.3
, pp. 837-851
-
-
Kumar, A.1
Rajendran, V.2
Sethumadhavan, R.3
Purohit, R.4
-
17
-
-
64649101249
-
Long-timescale molecular dynamics simulations of protein structure and function
-
Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE, (2009) Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol 19(2): 120-7.
-
(2009)
Curr Opin Struct Biol
, vol.19
, Issue.2
, pp. 120-127
-
-
Klepeis, J.L.1
Lindorff-Larsen, K.2
Dror, R.O.3
Shaw, D.E.4
-
18
-
-
58149200954
-
Database resources of the National Center for Biotechnology Information
-
Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 37: D5-15.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 5-15
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
-
19
-
-
0035173378
-
dbSNP: the NCBI database of genetic variation
-
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 308-311
-
-
Sherry, S.T.1
Ward, M.H.2
Kholodov, M.3
Baker, J.4
Phan, L.5
-
20
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucl Acids Res 28: 235-242.
-
(2000)
Nucl Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
21
-
-
0347383758
-
Modeller: generation and refinement of homology-based protein structure models
-
Fiser A, Sali A, (2003) Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 374: 461-491.
-
(2003)
Methods Enzymol
, vol.374
, pp. 461-491
-
-
Fiser, A.1
Sali, A.2
-
22
-
-
46249092554
-
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-
Hess B, Kutzner C, van der Spoel D, Lindahl E, (2008) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J Chem Theory Comput 4: 435-447.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
23
-
-
68149165614
-
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
-
Kumar P, Henikoff S, Ng PC, (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4: 1073-81.
-
(2009)
Nat Protoc
, vol.4
, pp. 1073-1081
-
-
Kumar, P.1
Henikoff, S.2
Ng, P.C.3
-
24
-
-
0035869223
-
Prediction of deleterious human alleles
-
Sunyaev S, Ramensky V, Koch I, Lathe W 3rd, Kondrashov AS, et al. (2011) Prediction of deleterious human alleles. Hum Mol Genet 10: 591-7.
-
(2011)
Hum Mol Genet
, vol.10
, pp. 591-597
-
-
Sunyaev, S.1
Ramensky, V.2
Koch, I.3
Lathe III, W.4
Kondrashov, A.S.5
-
25
-
-
33751013750
-
Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information
-
Capriotti E, Calabrese R, Casadio R, (2006) Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics 22: 2729-2734.
-
(2006)
Bioinformatics
, vol.22
, pp. 2729-2734
-
-
Capriotti, E.1
Calabrese, R.2
Casadio, R.3
-
26
-
-
25144496606
-
PMUT: a web-based tool for the annotation of pathological mutations on proteins
-
Ferrer-Costa C, Gelpí JL, Zamakola L, Parraga I, de la Cruz X, et al. (2005) PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics 21(14): 3176-8.
-
(2005)
Bioinformatics
, vol.21
, Issue.14
, pp. 3176-3178
-
-
Ferrer-Costa, C.1
Gelpí, J.L.2
Zamakola, L.3
Parraga, I.4
de la Cruz, X.5
-
27
-
-
70350671733
-
Automated inference of molecular mechanisms of disease from amino acid substitutions
-
Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, et al. (2009) Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 25: 2744-50.
-
(2009)
Bioinformatics
, vol.25
, pp. 2744-2750
-
-
Li, B.1
Krishnan, V.G.2
Mort, M.E.3
Xin, F.4
Kamati, K.K.5
-
28
-
-
80053297561
-
A new disease-specific machine learning approach for the prediction of cancer-causing missense variants
-
Capriotti E, Altman RB, (2011) A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. Genomics 98: 310-317.
-
(2011)
Genomics
, vol.98
, pp. 310-317
-
-
Capriotti, E.1
Altman, R.B.2
-
29
-
-
84878880551
-
Predicting the functional consequences of cancer-associated amino acid substitutions
-
Shihab HA, Gough J, Cooper DN, Day IN, Gaunt TR, (2013) Predicting the functional consequences of cancer-associated amino acid substitutions. Bioinformatics 29(12): 1504-10.
-
(2013)
Bioinformatics
, vol.29
, Issue.12
, pp. 1504-1510
-
-
Shihab, H.A.1
Gough, J.2
Cooper, D.N.3
Day, I.N.4
Gaunt, T.R.5
-
30
-
-
33747871385
-
SNP Function Portal: a web database for exploring the function implication of SNP alleles
-
Wang P, Dai M, Xuan W, McEachin RC, Jackson AU, et al. (2006) SNP Function Portal: a web database for exploring the function implication of SNP alleles. Bioinformatics 22(14): e523-9.
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Wang, P.1
Dai, M.2
Xuan, W.3
McEachin, R.C.4
Jackson, A.U.5
-
31
-
-
84861090227
-
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants
-
(Database issue): D935-9
-
De Baets G, Van Durme J, Reumers J, Maurer-Stroh S, Vanhee P,et al. (2012). SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Res. 40(Database issue): D935-9.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
De Baets, G.1
Van Durme, J.2
Reumers, J.3
Maurer-Stroh, S.4
Vanhee, P.5
-
32
-
-
84878535001
-
Cancer associated E17K mutation causes rapid conformational drift in AKT1 pleckstrin homology (PH) domain
-
Kumar A, Purohit R, (2013) Cancer associated E17K mutation causes rapid conformational drift in AKT1 pleckstrin homology (PH) domain. PLoS One 31;8(5): e64364.
-
(2013)
PLoS One
, vol.31
, Issue.5
-
-
Kumar, A.1
Purohit, R.2
-
33
-
-
0033578302
-
Cation-pi interactions in structural biology
-
Gallivan JP, Dougherty DA, (1999) Cation-pi interactions in structural biology. Proc Natl Acad Sci U S A 96(17): 9459-64.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, Issue.17
, pp. 9459-9464
-
-
Gallivan, J.P.1
Dougherty, D.A.2
-
34
-
-
23144441494
-
SRide: a server for identifying stabilizing residues in proteins
-
(Web Server issue):: W303-5
-
Magyar C, Gromiha MM, Pujadas G, Tusnády GE, Simon I (2005) SRide: a server for identifying stabilizing residues in proteins. Nucleic Acids Res. 33(Web Server issue): W303-5.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Magyar, C.1
Gromiha, M.M.2
Pujadas, G.3
Tusnády, G.E.4
Simon, I.5
-
35
-
-
0037442962
-
HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C, Boelens R, Bonvin AM, (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125: 1731-1737.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.3
-
36
-
-
77955391393
-
The HADDOCK web server for data-driven biomolecular docking
-
de Vries SJ, van Dijk M, Bonvin AMJJ, (2010) The HADDOCK web server for data-driven biomolecular docking. Nat. Protoc 5: 883-897.
-
(2010)
Nat. Protoc
, vol.5
, pp. 883-897
-
-
de Vries, S.J.1
van Dijk, M.2
Bonvin, A.M.J.J.3
-
37
-
-
0028907436
-
Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities
-
Nilges M, (1995) Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J Mol Biol 245: 645-660.
-
(1995)
J Mol Biol
, vol.245
, pp. 645-660
-
-
Nilges, M.1
-
38
-
-
0031566434
-
Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin
-
Nilges M, Macias MJ, O'Donoghue SI, Oschkinat H, (1997) Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol 269: 408-422.
-
(1997)
J Mol Biol
, vol.269
, pp. 408-422
-
-
Nilges, M.1
Macias, M.J.2
O'Donoghue, S.I.3
Oschkinat, H.4
-
39
-
-
3543012707
-
Crystallography and NMR system: a new software suite for macromolecular structure determination
-
Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, et al. (1998) Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta. Crystallogr. D. Biol. Crystallogr 54: 905-921.
-
(1998)
Acta. Crystallogr. D. Biol. Crystallogr
, vol.54
, pp. 905-921
-
-
Brünger, A.T.1
Adams, P.D.2
Clore, G.M.3
DeLano, W.L.4
Gros, P.5
-
40
-
-
84880943928
-
Computational Investigation of Cancer-Associated Molecular Mechanism in Aurora A (S155R) Mutation
-
Kumar A, Rajendran V, Sethumadhavan R, Purohit R, (2013) Computational Investigation of Cancer-Associated Molecular Mechanism in Aurora A (S155R) Mutation. Cell Biochem Biophys 66(3): 787-96.
-
(2013)
Cell Biochem Biophys
, vol.66
, Issue.3
, pp. 787-796
-
-
Kumar, A.1
Rajendran, V.2
Sethumadhavan, R.3
Purohit, R.4
-
41
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Dinola A, Haak JR, (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 8: 3684-3690.
-
(1984)
J Chem Phys
, vol.8
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
42
-
-
0029170114
-
Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins
-
Cheatham TE, Miller JL, Fox T, Darden TA, Kollman A, (1995) Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins. J Am Chem Soc 14: 4193-4194.
-
(1995)
J Am Chem Soc
, vol.14
, pp. 4193-4194
-
-
Cheatham, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, A.5
-
44
-
-
84855494872
-
Activation of Aurora A kinase by protein partner binding and phosphorylation are independent and synergistic
-
Dodson CA, Bayliss R, (2012) Activation of Aurora A kinase by protein partner binding and phosphorylation are independent and synergistic. J Biol Chem 287: 1150-1157.
-
(2012)
J Biol Chem
, vol.287
, pp. 1150-1157
-
-
Dodson, C.A.1
Bayliss, R.2
-
45
-
-
0037135979
-
Human TPX2 is required for targeting Aurora A kinase to the spindle
-
Kufer TA, Sillje HH, Korner R, Gruss OJ, Meraldi P, et al. (2002) Human TPX2 is required for targeting Aurora A kinase to the spindle. J Cell Biol 158: 617-623.
-
(2002)
J Cell Biol
, vol.158
, pp. 617-623
-
-
Kufer, T.A.1
Sillje, H.H.2
Korner, R.3
Gruss, O.J.4
Meraldi, P.5
-
46
-
-
84861790146
-
Computational investigation of pathogenic nsSNPs in CEP63 protein
-
Kumar A, Purohit R, (2012) Computational investigation of pathogenic nsSNPs in CEP63 protein. Gene 503(1): 75-82.
-
(2012)
Gene
, vol.503
, Issue.1
, pp. 75-82
-
-
Kumar, A.1
Purohit, R.2
|