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For: DasGupta D, Kaushik R, Jayaram B. From Ramachandran Maps to Tertiary Structures of Proteins. J Phys Chem B 2015;119:11136-45. [DOI: 10.1021/acs.jpcb.5b02999] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Number Cited by Other Article(s)
1
Ilyas M, Rahman A, Khan NH, Haroon M, Hussain H, Rehman L, Alam M, Rauf A, Waggas DS, Bawazeer S. Analysis of Germin-like protein genes family in Vitis vinifera (VvGLPs) using various in silico approaches. BRAZ J BIOL 2024;84:e256732. [DOI: 10.1590/1519-6984.256732] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/28/2021] [Indexed: 12/26/2022]  Open
2
Brown SM, Voráček V, Freeland S. What Would an Alien Amino Acid Alphabet Look Like and Why? ASTROBIOLOGY 2023;23:536-549. [PMID: 37022727 DOI: 10.1089/ast.2022.0107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
3
Mufassirin MMM, Newton MAH, Sattar A. Artificial intelligence for template-free protein structure prediction: a comprehensive review. Artif Intell Rev 2022. [DOI: 10.1007/s10462-022-10350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
4
Kaushik R, Zhang KY. An Integrated Protein Structure Fitness Scoring Approach for Identifying Native-Like Model Structures. Comput Struct Biotechnol J 2022;20:6467-6472. [DOI: 10.1016/j.csbj.2022.11.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]  Open
5
Pritam M, Singh G, Kumar R, Singh SP. Screening of potential antigens from whole proteome and development of multi-epitope vaccine against Rhizopus delemar using immunoinformatics approaches. J Biomol Struct Dyn 2022;41:2118-2145. [PMID: 35067195 DOI: 10.1080/07391102.2022.2028676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
6
Kaushik R, Zhang KYJ. ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures. Bioinformatics 2022;38:369-376. [PMID: 34542606 DOI: 10.1093/bioinformatics/btab666] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/06/2021] [Accepted: 09/16/2021] [Indexed: 02/03/2023]  Open
7
McTiernan TJ, Diaz DB, Saunders GJ, Sprang F, Yudin AK. Navigating complex peptide structures using macrocycle conformational maps. RSC Chem Biol 2022;3:739-747. [PMID: 35755184 PMCID: PMC9175111 DOI: 10.1039/d2cb00016d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/14/2022] [Indexed: 11/21/2022]  Open
8
Zhang R, Stahr MC, Kennedy MA. Introduction of a new scheme for classifying β-turns in protein structures. Proteins 2021;90:110-122. [PMID: 34322903 DOI: 10.1002/prot.26190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/11/2021] [Indexed: 11/09/2022]
9
Bhat R, Kaushik R, Singh A, DasGupta D, Jayaraj A, Soni A, Shandilya A, Shekhar V, Shekhar S, Jayaram B. A comprehensive automated computer-aided discovery pipeline from genomes to hit molecules. Chem Eng Sci 2020. [DOI: 10.1016/j.ces.2020.115711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
10
Ghavimi R, Mohammadi E, Akbari V, Shafiee F, Jahanian-Najafabadi A. In silico design of two novel fusion proteins, p28-IL-24 and p28-M4, targeted to breast cancer cells. Res Pharm Sci 2020;15:200-208. [PMID: 32582360 PMCID: PMC7306244 DOI: 10.4103/1735-5362.283820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/20/2020] [Accepted: 04/18/2020] [Indexed: 01/29/2023]  Open
11
Kaushik R, Zhang KYJ. A protein sequence fitness function for identifying natural and nonnatural proteins. Proteins 2020;88:1271-1284. [PMID: 32415863 DOI: 10.1002/prot.25900] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/26/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022]
12
Computational approaches for drug discovery against trypanosomatid-caused diseases. Parasitology 2020;147:611-633. [DOI: 10.1017/s0031182020000207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
13
Ravikumar A, Ramakrishnan C, Srinivasan N. Stereochemical Assessment of (φ,ψ) Outliers in Protein Structures Using Bond Geometry-Specific Ramachandran Steric-Maps. Structure 2019;27:1875-1884.e2. [PMID: 31607615 DOI: 10.1016/j.str.2019.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/23/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
14
Mehmankhah M, Bhat R, Anvar MS, Ali S, Alam A, Farooqui A, Amir F, Anwer A, Khan S, Azmi I, Ali R, Ishrat R, Hassan MI, Minuchehr Z, Kazim SN. Structure-Guided Approach to Identify Potential Inhibitors of Large Envelope Protein to Prevent Hepatitis B Virus Infection. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019;2019:1297484. [PMID: 31772697 PMCID: PMC6854180 DOI: 10.1155/2019/1297484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/10/2019] [Accepted: 07/02/2019] [Indexed: 01/05/2023]
15
Kaushik R, Singh A, Jayaram B. Where Informatics Lags Chemistry Leads. Biochemistry 2017;57:503-506. [DOI: 10.1021/acs.biochem.7b01073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
16
DasGupta D, Mandalaparthy V, Jayaram B. A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level. J Comput Chem 2017;38:2791-2801. [PMID: 28940242 DOI: 10.1002/jcc.25072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/27/2017] [Accepted: 09/01/2017] [Indexed: 02/05/2023]
17
Saravanan KM, Selvaraj S. Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins. J Biol Phys 2017;43:265-278. [PMID: 28577238 PMCID: PMC5471173 DOI: 10.1007/s10867-017-9451-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 04/13/2017] [Indexed: 12/22/2022]  Open
18
Ponnuraj K, Saravanan KM. Dihedral angle preferences of DNA and RNA binding amino acid residues in proteins. Int J Biol Macromol 2017;97:434-439. [PMID: 28099891 DOI: 10.1016/j.ijbiomac.2017.01.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 11/30/2022]
19
Das Gupta D, Kaushik R, Jayaram B. Protein folding is a convergent problem! Biochem Biophys Res Commun 2016;480:741-744. [DOI: 10.1016/j.bbrc.2016.10.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/27/2016] [Indexed: 11/25/2022]
20
Kaushik R, Jayaram B. Structural difficulty index: a reliable measure for modelability of protein tertiary structures. Protein Eng Des Sel 2016;29:391-7. [PMID: 27334454 DOI: 10.1093/protein/gzw025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/27/2016] [Indexed: 11/13/2022]  Open
21
Borguesan B, e Silva MB, Grisci B, Inostroza-Ponta M, Dorn M. APL: An angle probability list to improve knowledge-based metaheuristics for the three-dimensional protein structure prediction. Comput Biol Chem 2015;59 Pt A:142-57. [DOI: 10.1016/j.compbiolchem.2015.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 08/05/2015] [Accepted: 08/17/2015] [Indexed: 10/23/2022]
22
ProTSAV: A protein tertiary structure analysis and validation server. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015;1864:11-9. [PMID: 26478257 DOI: 10.1016/j.bbapap.2015.10.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/26/2015] [Accepted: 10/14/2015] [Indexed: 01/06/2023]
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