K G Tina, R Bhadra, N Srinivasan. Nucleic Acids Res 2007
Times Cited: 638
Times Cited: 638
Times Cited
Times Co-cited
Similarity
UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
17
The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
15
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.
Markus Wiederstein, Manfred J Sippl. Nucleic Acids Res 2007
Markus Wiederstein, Manfred J Sippl. Nucleic Acids Res 2007
11
The Phyre2 web portal for protein modeling, prediction and analysis.
Lawrence A Kelley, Stefans Mezulis, Christopher M Yates, Mark N Wass, Michael J E Sternberg. Nat Protoc 2015
Lawrence A Kelley, Stefans Mezulis, Christopher M Yates, Mark N Wass, Michael J E Sternberg. Nat Protoc 2015
11
The ClusPro web server for protein-protein docking.
Dima Kozakov, David R Hall, Bing Xia, Kathryn A Porter, Dzmitry Padhorny, Christine Yueh, Dmitri Beglov, Sandor Vajda. Nat Protoc 2017
Dima Kozakov, David R Hall, Bing Xia, Kathryn A Porter, Dzmitry Padhorny, Christine Yueh, Dmitri Beglov, Sandor Vajda. Nat Protoc 2017
10
Inference of macromolecular assemblies from crystalline state.
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
10
The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.
G C P van Zundert, J P G L M Rodrigues, M Trellet, C Schmitz, P L Kastritis, E Karaca, A S J Melquiond, M van Dijk, S J de Vries, A M J J Bonvin. J Mol Biol 2016
G C P van Zundert, J P G L M Rodrigues, M Trellet, C Schmitz, P L Kastritis, E Karaca, A S J Melquiond, M van Dijk, S J de Vries, A M J J Bonvin. J Mol Biol 2016
9
Verification of protein structures: patterns of nonbonded atomic interactions.
C Colovos, T O Yeates. Protein Sci 1993
C Colovos, T O Yeates. Protein Sci 1993
9
SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
9
Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
9
Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.
Jun Lan, Jiwan Ge, Jinfang Yu, Sisi Shan, Huan Zhou, Shilong Fan, Qi Zhang, Xuanling Shi, Qisheng Wang, Linqi Zhang,[...]. Nature 2020
Jun Lan, Jiwan Ge, Jinfang Yu, Sisi Shan, Huan Zhou, Shilong Fan, Qi Zhang, Xuanling Shi, Qisheng Wang, Linqi Zhang,[...]. Nature 2020
8
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.
Li C Xue, João Pglm Rodrigues, Panagiotis L Kastritis, Alexandre Mjj Bonvin, Anna Vangone. Bioinformatics 2016
Li C Xue, João Pglm Rodrigues, Panagiotis L Kastritis, Alexandre Mjj Bonvin, Anna Vangone. Bioinformatics 2016
8
REFMAC5 for the refinement of macromolecular crystal structures.
Garib N Murshudov, Pavol Skubák, Andrey A Lebedev, Navraj S Pannu, Roberto A Steiner, Robert A Nicholls, Martyn D Winn, Fei Long, Alexei A Vagin. Acta Crystallogr D Biol Crystallogr 2011
Garib N Murshudov, Pavol Skubák, Andrey A Lebedev, Navraj S Pannu, Roberto A Steiner, Robert A Nicholls, Martyn D Winn, Fei Long, Alexei A Vagin. Acta Crystallogr D Biol Crystallogr 2011
8
TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
8
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
W Kabsch, C Sander. Biopolymers 1983
W Kabsch, C Sander. Biopolymers 1983
7
Deciphering key features in protein structures with the new ENDscript server.
Xavier Robert, Patrice Gouet. Nucleic Acids Res 2014
Xavier Robert, Patrice Gouet. Nucleic Acids Res 2014
7
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
7
Comparative protein modelling by satisfaction of spatial restraints.
A Sali, T L Blundell. J Mol Biol 1993
A Sali, T L Blundell. J Mol Biol 1993
7
The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
7
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
6
GROMACS: fast, flexible, and free.
David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E Mark, Herman J C Berendsen. J Comput Chem 2005
David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E Mark, Herman J C Berendsen. J Comput Chem 2005
6
MolProbity: all-atom structure validation for macromolecular crystallography.
Vincent B Chen, W Bryan Arendall, Jeffrey J Headd, Daniel A Keedy, Robert M Immormino, Gary J Kapral, Laura W Murray, Jane S Richardson, David C Richardson. Acta Crystallogr D Biol Crystallogr 2010
Vincent B Chen, W Bryan Arendall, Jeffrey J Headd, Daniel A Keedy, Robert M Immormino, Gary J Kapral, Laura W Murray, Jane S Richardson, David C Richardson. Acta Crystallogr D Biol Crystallogr 2010
6
Phaser crystallographic software.
Airlie J McCoy, Ralf W Grosse-Kunstleve, Paul D Adams, Martyn D Winn, Laurent C Storoni, Randy J Read. J Appl Crystallogr 2007
Airlie J McCoy, Ralf W Grosse-Kunstleve, Paul D Adams, Martyn D Winn, Laurent C Storoni, Randy J Read. J Appl Crystallogr 2007
6
Overview of the CCP4 suite and current developments.
Martyn D Winn, Charles C Ballard, Kevin D Cowtan, Eleanor J Dodson, Paul Emsley, Phil R Evans, Ronan M Keegan, Eugene B Krissinel, Andrew G W Leslie, Airlie McCoy,[...]. Acta Crystallogr D Biol Crystallogr 2011
Martyn D Winn, Charles C Ballard, Kevin D Cowtan, Eleanor J Dodson, Paul Emsley, Phil R Evans, Ronan M Keegan, Eugene B Krissinel, Andrew G W Leslie, Airlie McCoy,[...]. Acta Crystallogr D Biol Crystallogr 2011
6
The EMBL-EBI search and sequence analysis tools APIs in 2019.
Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R N Tivey, Simon C Potter, Robert D Finn,[...]. Nucleic Acids Res 2019
Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R N Tivey, Simon C Potter, Robert D Finn,[...]. Nucleic Acids Res 2019
6
Highly accurate protein structure prediction with AlphaFold.
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
6
Comparative Protein Structure Modeling Using MODELLER.
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
5
Towards automated crystallographic structure refinement with phenix.refine.
Pavel V Afonine, Ralf W Grosse-Kunstleve, Nathaniel Echols, Jeffrey J Headd, Nigel W Moriarty, Marat Mustyakimov, Thomas C Terwilliger, Alexandre Urzhumtsev, Peter H Zwart, Paul D Adams. Acta Crystallogr D Biol Crystallogr 2012
Pavel V Afonine, Ralf W Grosse-Kunstleve, Nathaniel Echols, Jeffrey J Headd, Nigel W Moriarty, Marat Mustyakimov, Thomas C Terwilliger, Alexandre Urzhumtsev, Peter H Zwart, Paul D Adams. Acta Crystallogr D Biol Crystallogr 2012
5
[20] Processing of X-ray diffraction data collected in oscillation mode.
Zbyszek Otwinowski, Wladek Minor. Methods Enzymol 1997
Zbyszek Otwinowski, Wladek Minor. Methods Enzymol 1997
5
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.
Oleg Trott, Arthur J Olson. J Comput Chem 2010
Oleg Trott, Arthur J Olson. J Comput Chem 2010
5
The HDOCK server for integrated protein-protein docking.
Yumeng Yan, Huanyu Tao, Jiahua He, Sheng-You Huang. Nat Protoc 2020
Yumeng Yan, Huanyu Tao, Jiahua He, Sheng-You Huang. Nat Protoc 2020
5
Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.
Daniel Wrapp, Nianshuang Wang, Kizzmekia S Corbett, Jory A Goldsmith, Ching-Lin Hsieh, Olubukola Abiona, Barney S Graham, Jason S McLellan. Science 2020
Daniel Wrapp, Nianshuang Wang, Kizzmekia S Corbett, Jory A Goldsmith, Ching-Lin Hsieh, Olubukola Abiona, Barney S Graham, Jason S McLellan. Science 2020
5
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2016
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2016
5
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.
Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
5
The FoldX web server: an online force field.
Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. Nucleic Acids Res 2005
Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. Nucleic Acids Res 2005
5
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
N Guex, M C Peitsch. Electrophoresis 1997
N Guex, M C Peitsch. Electrophoresis 1997
5
MolProbity: More and better reference data for improved all-atom structure validation.
Christopher J Williams, Jeffrey J Headd, Nigel W Moriarty, Michael G Prisant, Lizbeth L Videau, Lindsay N Deis, Vishal Verma, Daniel A Keedy, Bradley J Hintze, Vincent B Chen,[...]. Protein Sci 2018
Christopher J Williams, Jeffrey J Headd, Nigel W Moriarty, Michael G Prisant, Lizbeth L Videau, Lindsay N Deis, Vishal Verma, Daniel A Keedy, Bradley J Hintze, Vincent B Chen,[...]. Protein Sci 2018
5
LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
5
Computational alanine scanning of protein-protein interfaces.
Tanja Kortemme, David E Kim, David Baker. Sci STKE 2004
Tanja Kortemme, David E Kim, David Baker. Sci STKE 2004
4
Protein Structure and Function Prediction Using I-TASSER.
Jianyi Yang, Yang Zhang. Curr Protoc Bioinformatics 2015
Jianyi Yang, Yang Zhang. Curr Protoc Bioinformatics 2015
4
A method and server for predicting damaging missense mutations.
Ivan A Adzhubei, Steffen Schmidt, Leonid Peshkin, Vasily E Ramensky, Anna Gerasimova, Peer Bork, Alexey S Kondrashov, Shamil R Sunyaev. Nat Methods 2010
Ivan A Adzhubei, Steffen Schmidt, Leonid Peshkin, Vasily E Ramensky, Anna Gerasimova, Peer Bork, Alexey S Kondrashov, Shamil R Sunyaev. Nat Methods 2010
4
SIFT web server: predicting effects of amino acid substitutions on proteins.
Ngak-Leng Sim, Prateek Kumar, Jing Hu, Steven Henikoff, Georg Schneider, Pauline C Ng. Nucleic Acids Res 2012
Ngak-Leng Sim, Prateek Kumar, Jing Hu, Steven Henikoff, Georg Schneider, Pauline C Ng. Nucleic Acids Res 2012
4
HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.
Cyril Dominguez, Rolf Boelens, Alexandre M J J Bonvin. J Am Chem Soc 2003
Cyril Dominguez, Rolf Boelens, Alexandre M J J Bonvin. J Am Chem Soc 2003
4
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability.
Carlos Hm Rodrigues, Douglas Ev Pires, David B Ascher. Nucleic Acids Res 2018
Carlos Hm Rodrigues, Douglas Ev Pires, David B Ascher. Nucleic Acids Res 2018
4
Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2.
Qihui Wang, Yanfang Zhang, Lili Wu, Sheng Niu, Chunli Song, Zengyuan Zhang, Guangwen Lu, Chengpeng Qiao, Yu Hu, Kwok-Yung Yuen,[...]. Cell 2020
Qihui Wang, Yanfang Zhang, Lili Wu, Sheng Niu, Chunli Song, Zengyuan Zhang, Guangwen Lu, Chengpeng Qiao, Yu Hu, Kwok-Yung Yuen,[...]. Cell 2020
4
g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.
Rashmi Kumari, Rajendra Kumar, Andrew Lynn. J Chem Inf Model 2014
Rashmi Kumari, Rajendra Kumar, Andrew Lynn. J Chem Inf Model 2014
4
PatchDock and SymmDock: servers for rigid and symmetric docking.
Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J Wolfson. Nucleic Acids Res 2005
Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J Wolfson. Nucleic Acids Res 2005
4
Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.