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For: Kosciolek T, Jones DT. De novo structure prediction of globular proteins aided by sequence variation-derived contacts. PLoS One 2014;9:e92197. [PMID: 24637808 PMCID: PMC3956894 DOI: 10.1371/journal.pone.0092197] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/19/2014] [Indexed: 12/21/2022]  Open
Number Cited by Other Article(s)
1
Gelman S, Johnson B, Freschlin C, Sharma A, D'Costa S, Peters J, Gitter A, Romero PA. Biophysics-based protein language models for protein engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.03.15.585128. [PMID: 38559182 PMCID: PMC10980077 DOI: 10.1101/2024.03.15.585128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
2
Hasan M, Ahmed S, Imranuzzaman M, Bari R, Roy S, Hasan MM, Mia MM. Designing and development of efficient multi-epitope-based peptide vaccine candidate against emerging avian rotavirus strains: A vaccinomic approach. J Genet Eng Biotechnol 2024;22:100398. [PMID: 39179326 PMCID: PMC11260576 DOI: 10.1016/j.jgeb.2024.100398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/17/2024] [Accepted: 06/19/2024] [Indexed: 08/26/2024]
3
Patkar SS, Wang B, Mosquera AM, Kiick KL. Genetically Fusing Order-Promoting and Thermoresponsive Building Blocks to Design Hybrid Biomaterials. Chemistry 2024;30:e202400582. [PMID: 38501912 PMCID: PMC11661552 DOI: 10.1002/chem.202400582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/20/2024]
4
Rahman MN, Ahmed S, Hasan M, Shuvo MSA, Islam MA, Hasan R, Roy S, Hossain H, Mia MM. Immunoselective progression of a multi-epitope-based subunit vaccine candidate to convey protection against the parasite Onchocerca lupi. INFORMATICS IN MEDICINE UNLOCKED 2023. [DOI: 10.1016/j.imu.2023.101209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]  Open
5
Hasan M, Mia M. Exploratory Algorithm of a Multi-epitope-based Subunit Vaccine Candidate Against Cryptosporidium hominis: Reverse Vaccinology-Based Immunoinformatic Approach. Int J Pept Res Ther 2022;28:134. [PMID: 35911179 PMCID: PMC9315849 DOI: 10.1007/s10989-022-10438-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2022] [Indexed: 12/03/2022]
6
Liu J, Zhao KL, He GX, Wang LJ, Zhou XG, Zhang GJ. A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization. Bioinformatics 2021;38:99-107. [PMID: 34459867 DOI: 10.1093/bioinformatics/btab620] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/23/2021] [Accepted: 08/25/2021] [Indexed: 02/03/2023]  Open
7
Hou M, Peng C, Zhou X, Zhang B, Zhang G. Multi contact-based folding method for de novo protein structure prediction. Brief Bioinform 2021;23:6445108. [PMID: 34849573 DOI: 10.1093/bib/bbab463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/21/2021] [Accepted: 10/10/2021] [Indexed: 11/12/2022]  Open
8
Munro LJ, Kell DB. Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021;478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
9
Lara Ortiz MT, Martinell García V, Del Rio G. Saturation Mutagenesis of the Transmembrane Region of HokC in Escherichia coli Reveals Its High Tolerance to Mutations. Int J Mol Sci 2021;22:ijms221910359. [PMID: 34638709 PMCID: PMC8509063 DOI: 10.3390/ijms221910359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022]  Open
10
Mia MM, Hasan M, Hasan MM, Khan SS, Rahman MN, Ahmed S, Basak A, Sakib MN, Banik S. Multi-epitope based subunit vaccine construction against Banna virus targeting on two outer proteins (VP4 and VP9): A computational approach. INFECTION GENETICS AND EVOLUTION 2021;95:105076. [PMID: 34500093 DOI: 10.1016/j.meegid.2021.105076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/28/2021] [Accepted: 09/03/2021] [Indexed: 11/17/2022]
11
Foroutan B, Abbasian Najafabadi AR. Capabilities of bioinformatics tools for optimizing physicochemical features of proteins used in Nano biosensors: A short overview of the tools related to bioinformatics. Biochem Biophys Rep 2021;27:101094. [PMID: 34401530 PMCID: PMC8350186 DOI: 10.1016/j.bbrep.2021.101094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/27/2022]  Open
12
Reza MS, Zhang H, Hossain MT, Jin L, Feng S, Wei Y. COMTOP: Protein Residue-Residue Contact Prediction through Mixed Integer Linear Optimization. MEMBRANES 2021;11:membranes11070503. [PMID: 34209399 PMCID: PMC8305966 DOI: 10.3390/membranes11070503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022]
13
Zhang H, Bei Z, Xi W, Hao M, Ju Z, Saravanan KM, Zhang H, Guo N, Wei Y. Evaluation of residue-residue contact prediction methods: From retrospective to prospective. PLoS Comput Biol 2021;17:e1009027. [PMID: 34029314 PMCID: PMC8177648 DOI: 10.1371/journal.pcbi.1009027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/04/2021] [Accepted: 04/28/2021] [Indexed: 12/31/2022]  Open
14
Machine learning in protein structure prediction. Curr Opin Chem Biol 2021;65:1-8. [PMID: 34015749 DOI: 10.1016/j.cbpa.2021.04.005] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/10/2021] [Indexed: 12/31/2022]
15
Abbass J, Nebel JC. Rosetta and the Journey to Predict Proteins’ Structures, 20 Years on. Curr Bioinform 2020. [DOI: 10.2174/1574893615999200504103643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
16
Zhang GJ, Wang XQ, Ma LF, Wang LJ, Hu J, Zhou XG. Two-Stage Distance Feature-based Optimization Algorithm for De novo Protein Structure Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:2119-2130. [PMID: 31107659 DOI: 10.1109/tcbb.2019.2917452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
17
Liu J, Zhou XG, Zhang Y, Zhang GJ. CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. Bioinformatics 2020;36:2443-2450. [PMID: 31860059 DOI: 10.1093/bioinformatics/btz943] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 12/27/2022]  Open
18
Hasan M, Azim KF, Imran MAS, Chowdhury IM, Urme SRA, Parvez MSA, Uddin MB, Ahmed SSU. Comprehensive genome based analysis of Vibrio parahaemolyticus for identifying novel drug and vaccine molecules: Subtractive proteomics and vaccinomics approach. PLoS One 2020;15:e0237181. [PMID: 32813697 PMCID: PMC7444560 DOI: 10.1371/journal.pone.0237181] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023]  Open
19
Zhang GJ, Ma LF, Wang XQ, Zhou XG. Secondary Structure and Contact Guided Differential Evolution for Protein Structure Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:1068-1081. [PMID: 30295627 DOI: 10.1109/tcbb.2018.2873691] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
20
Abbass J, Nebel JC. Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure. BMC Bioinformatics 2020;21:170. [PMID: 32357827 PMCID: PMC7195757 DOI: 10.1186/s12859-020-3491-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/13/2020] [Indexed: 11/10/2022]  Open
21
Lesk AM. Not Enough Natural Data? Sequence and Ye Shall Find. Front Mol Biosci 2020;7:65. [PMID: 32373628 PMCID: PMC7186298 DOI: 10.3389/fmolb.2020.00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/25/2020] [Indexed: 11/28/2022]  Open
22
Lemke T, Berg A, Jain A, Peter C. EncoderMap(II): Visualizing Important Molecular Motions with Improved Generation of Protein Conformations. J Chem Inf Model 2019;59:4550-4560. [PMID: 31647645 DOI: 10.1021/acs.jcim.9b00675] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
23
Wozniak PP, Pelc J, Skrzypecki M, Vriend G, Kotulska M. Bio-knowledge-based filters improve residue-residue contact prediction accuracy. Bioinformatics 2019;34:3675-3683. [PMID: 29850768 DOI: 10.1093/bioinformatics/bty416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 05/19/2018] [Indexed: 11/13/2022]  Open
24
Kandathil SM, Greener JG, Jones DT. Recent developments in deep learning applied to protein structure prediction. Proteins 2019;87:1179-1189. [PMID: 31589782 PMCID: PMC6899861 DOI: 10.1002/prot.25824] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 12/29/2022]
25
Greener JG, Kandathil SM, Jones DT. Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints. Nat Commun 2019;10:3977. [PMID: 31484923 PMCID: PMC6726615 DOI: 10.1038/s41467-019-11994-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/14/2019] [Indexed: 01/30/2023]  Open
26
Hasan M, Islam S, Chakraborty S, Mustafa AH, Azim KF, Joy ZF, Hossain MN, Foysal SH, Hasan MN. Contriving a chimeric polyvalent vaccine to prevent infections caused by herpes simplex virus (type-1 and type-2): an exploratory immunoinformatic approach. J Biomol Struct Dyn 2019;38:2898-2915. [PMID: 31328668 DOI: 10.1080/07391102.2019.1647286] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
27
Marks C, Deane CM. Increasing the accuracy of protein loop structure prediction with evolutionary constraints. Bioinformatics 2019;35:2585-2592. [PMID: 30535347 DOI: 10.1093/bioinformatics/bty996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/28/2018] [Accepted: 12/07/2018] [Indexed: 11/12/2022]  Open
28
Rollins NJ, Brock KP, Poelwijk FJ, Stiffler MA, Gauthier NP, Sander C, Marks DS. Inferring protein 3D structure from deep mutation scans. Nat Genet 2019;51:1170-1176. [PMID: 31209393 PMCID: PMC7295002 DOI: 10.1038/s41588-019-0432-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/29/2019] [Indexed: 11/09/2022]
29
Azim KF, Hasan M, Hossain MN, Somana SR, Hoque SF, Bappy MNI, Chowdhury AT, Lasker T. Immunoinformatics approaches for designing a novel multi epitope peptide vaccine against human norovirus (Norwalk virus). INFECTION GENETICS AND EVOLUTION 2019;74:103936. [PMID: 31233780 DOI: 10.1016/j.meegid.2019.103936] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 12/19/2022]
30
Wu Q, Peng Z, Anishchenko I, Cong Q, Baker D, Yang J. Protein contact prediction using metagenome sequence data and residual neural networks. Bioinformatics 2019;36:41-48. [PMID: 31173061 PMCID: PMC8792440 DOI: 10.1093/bioinformatics/btz477] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 05/30/2019] [Accepted: 06/04/2019] [Indexed: 01/31/2023]  Open
31
Hasan M, Azim KF, Begum A, Khan NA, Shammi TS, Imran AS, Chowdhury IM, Urme SRA. Vaccinomics strategy for developing a unique multi-epitope monovalent vaccine against Marburg marburgvirus. INFECTION GENETICS AND EVOLUTION 2019;70:140-157. [DOI: 10.1016/j.meegid.2019.03.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/09/2019] [Accepted: 03/04/2019] [Indexed: 12/23/2022]
32
Adhikari B, Hou J, Cheng J. DNCON2: improved protein contact prediction using two-level deep convolutional neural networks. Bioinformatics 2019;34:1466-1472. [PMID: 29228185 PMCID: PMC5925776 DOI: 10.1093/bioinformatics/btx781] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/07/2017] [Indexed: 12/14/2022]  Open
33
Hasan M, Ghosh PP, Azim KF, Mukta S, Abir RA, Nahar J, Hasan Khan MM. Reverse vaccinology approach to design a novel multi-epitope subunit vaccine against avian influenza A (H7N9) virus. Microb Pathog 2019;130:19-37. [PMID: 30822457 DOI: 10.1016/j.micpath.2019.02.023] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/18/2022]
34
MacCarthy E, Perry D, Kc DB. Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction. Methods Mol Biol 2019;1958:15-45. [PMID: 30945212 DOI: 10.1007/978-1-4939-9161-7_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
35
Wan C. Background on Biology of Ageing and Bioinformatics. ADVANCED INFORMATION AND KNOWLEDGE PROCESSING 2019:25-43. [DOI: 10.1007/978-3-319-97919-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
36
Vorberg S, Seemayer S, Söding J. Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction. PLoS Comput Biol 2018;14:e1006526. [PMID: 30395601 PMCID: PMC6237422 DOI: 10.1371/journal.pcbi.1006526] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/15/2018] [Accepted: 09/24/2018] [Indexed: 12/01/2022]  Open
37
Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings. Int J Mol Sci 2018;19:ijms19113315. [PMID: 30366362 PMCID: PMC6274761 DOI: 10.3390/ijms19113315] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 12/22/2022]  Open
38
Jones DT, Kandathil SM. High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features. Bioinformatics 2018;34:3308-3315. [PMID: 29718112 PMCID: PMC6157083 DOI: 10.1093/bioinformatics/bty341] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/06/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022]  Open
39
Kandathil SM, Garza-Fabre M, Handl J, Lovell SC. Improved fragment-based protein structure prediction by redesign of search heuristics. Sci Rep 2018;8:13694. [PMID: 30209258 PMCID: PMC6135816 DOI: 10.1038/s41598-018-31891-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/22/2018] [Indexed: 11/09/2022]  Open
40
de Oliveira SHP, Shi J, Deane CM. Comparing co-evolution methods and their application to template-free protein structure prediction. Bioinformatics 2018;33:373-381. [PMID: 28171606 PMCID: PMC5860252 DOI: 10.1093/bioinformatics/btw618] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 09/19/2016] [Accepted: 09/22/2016] [Indexed: 02/01/2023]  Open
41
Solanki V, Tiwari V. Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii. Sci Rep 2018;8:9044. [PMID: 29899345 PMCID: PMC5997985 DOI: 10.1038/s41598-018-26689-7] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/17/2018] [Indexed: 11/24/2022]  Open
42
de Oliveira SHP, Law EC, Shi J, Deane CM. Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction. Bioinformatics 2018;34:1132-1140. [PMID: 29136098 PMCID: PMC6030820 DOI: 10.1093/bioinformatics/btx722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 09/22/2017] [Accepted: 11/04/2017] [Indexed: 01/12/2023]  Open
43
Xu C, Bouvier G, Bardiaux B, Nilges M, Malliavin T, Lisser A. Ordering Protein Contact Matrices. Comput Struct Biotechnol J 2018;16:140-156. [PMID: 29632657 PMCID: PMC5889711 DOI: 10.1016/j.csbj.2018.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 11/29/2022]  Open
44
dos Santos RN, Ferrari AJR, de Jesus HCR, Gozzo FC, Morcos F, Martínez L. Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals. Bioinformatics 2018;34:2201-2208. [DOI: 10.1093/bioinformatics/bty074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/10/2018] [Indexed: 11/13/2022]  Open
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Li B, Fooksa M, Heinze S, Meiler J. Finding the needle in the haystack: towards solving the protein-folding problem computationally. Crit Rev Biochem Mol Biol 2018;53:1-28. [PMID: 28976219 PMCID: PMC6790072 DOI: 10.1080/10409238.2017.1380596] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/22/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022]
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Adhikari B, Cheng J. CONFOLD2: improved contact-driven ab initio protein structure modeling. BMC Bioinformatics 2018;19:22. [PMID: 29370750 PMCID: PMC5784681 DOI: 10.1186/s12859-018-2032-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 01/17/2018] [Indexed: 12/31/2022]  Open
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Prediction of Structures and Interactions from Genome Information. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018;1105:123-152. [DOI: 10.1007/978-981-13-2200-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Zhang C, Mortuza SM, He B, Wang Y, Zhang Y. Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12. Proteins 2017;86 Suppl 1:136-151. [PMID: 29082551 DOI: 10.1002/prot.25414] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/09/2017] [Accepted: 10/27/2017] [Indexed: 12/26/2022]
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Systematic Identification of Machine-Learning Models Aimed to Classify Critical Residues for Protein Function from Protein Structure. Molecules 2017;22:molecules22101673. [PMID: 28991206 PMCID: PMC6151554 DOI: 10.3390/molecules22101673] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/24/2017] [Accepted: 09/24/2017] [Indexed: 12/14/2022]  Open
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Buchan DWA, Jones DT. EigenTHREADER: analogous protein fold recognition by efficient contact map threading. Bioinformatics 2017;33:2684-2690. [PMID: 28419258 PMCID: PMC5860056 DOI: 10.1093/bioinformatics/btx217] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/18/2017] [Accepted: 04/12/2017] [Indexed: 11/13/2022]  Open
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