W Kabsch, C Sander. Biopolymers 1983
Times Cited: 10815
Times Cited: 10815
Times Cited
Times Co-cited
Similarity
Canonical sampling through velocity rescaling.
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
22
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
21
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
20
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
12
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
10
A series of PDB-related databanks for everyday needs.
Wouter G Touw, Coos Baakman, Jon Black, Tim A H te Beek, E Krieger, Robbie P Joosten, Gert Vriend. Nucleic Acids Res 2015
Wouter G Touw, Coos Baakman, Jon Black, Tim A H te Beek, E Krieger, Robbie P Joosten, Gert Vriend. Nucleic Acids Res 2015
10
CHARMM36m: an improved force field for folded and intrinsically disordered proteins.
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L de Groot, Helmut Grubmüller, Alexander D MacKerell. Nat Methods 2017
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L de Groot, Helmut Grubmüller, Alexander D MacKerell. Nat Methods 2017
10
Improved protein structure prediction using predicted interresidue orientations.
Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker. Proc Natl Acad Sci U S A 2020
Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker. Proc Natl Acad Sci U S A 2020
8
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
8
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
A series of PDB related databases for everyday needs.
Robbie P Joosten, Tim A H te Beek, Elmar Krieger, Maarten L Hekkelman, Rob W W Hooft, Reinhard Schneider, Chris Sander, Gert Vriend. Nucleic Acids Res 2011
Robbie P Joosten, Tim A H te Beek, Elmar Krieger, Maarten L Hekkelman, Rob W W Hooft, Reinhard Schneider, Chris Sander, Gert Vriend. Nucleic Acids Res 2011
7
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
7
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation.
Berk Hess. J Chem Theory Comput 2008
Berk Hess. J Chem Theory Comput 2008
7
Accurate prediction of protein structures and interactions using a three-track neural network.
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer,[...]. Science 2021
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer,[...]. Science 2021
7
Highly accurate protein structure prediction for the human proteome.
Kathryn Tunyasuvunakool, Jonas Adler, Zachary Wu, Tim Green, Michal Zielinski, Augustin Žídek, Alex Bridgland, Andrew Cowie, Clemens Meyer, Agata Laydon,[...]. Nature 2021
Kathryn Tunyasuvunakool, Jonas Adler, Zachary Wu, Tim Green, Michal Zielinski, Augustin Žídek, Alex Bridgland, Andrew Cowie, Clemens Meyer, Agata Laydon,[...]. Nature 2021
7
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl. J Chem Theory Comput 2008
Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl. J Chem Theory Comput 2008
6
Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
6
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
CD-HIT: accelerated for clustering the next-generation sequencing data.
Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li. Bioinformatics 2012
Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li. Bioinformatics 2012
5
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
5
BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra.
András Micsonai, Frank Wien, Éva Bulyáki, Judit Kun, Éva Moussong, Young-Ho Lee, Yuji Goto, Matthieu Réfrégiers, József Kardos. Nucleic Acids Res 2018
András Micsonai, Frank Wien, Éva Bulyáki, Judit Kun, Éva Moussong, Young-Ho Lee, Yuji Goto, Matthieu Réfrégiers, József Kardos. Nucleic Acids Res 2018
5
Improved side-chain torsion potentials for the Amber ff99SB protein force field.
Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L Klepeis, Ron O Dror, David E Shaw. Proteins 2010
Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L Klepeis, Ron O Dror, David E Shaw. Proteins 2010
5
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
5
DisProt: intrinsic protein disorder annotation in 2020.
András Hatos, Borbála Hajdu-Soltész, Alexander M Monzon, Nicolas Palopoli, Lucía Álvarez, Burcu Aykac-Fas, Claudio Bassot, Guillermo I Benítez, Martina Bevilacqua, Anastasia Chasapi,[...]. Nucleic Acids Res 2020
András Hatos, Borbála Hajdu-Soltész, Alexander M Monzon, Nicolas Palopoli, Lucía Álvarez, Burcu Aykac-Fas, Claudio Bassot, Guillermo I Benítez, Martina Bevilacqua, Anastasia Chasapi,[...]. Nucleic Acids Res 2020
5
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
5
Biopython: freely available Python tools for computational molecular biology and bioinformatics.
Peter J A Cock, Tiago Antao, Jeffrey T Chang, Brad A Chapman, Cymon J Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski,[...]. Bioinformatics 2009
Peter J A Cock, Tiago Antao, Jeffrey T Chang, Brad A Chapman, Cymon J Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski,[...]. Bioinformatics 2009
5
Improved protein structure prediction using potentials from deep learning.
Andrew W Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander W R Nelson, Alex Bridgland,[...]. Nature 2020
Andrew W Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander W R Nelson, Alex Bridgland,[...]. Nature 2020
5
Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations.
Suman Samantray, Feng Yin, Batuhan Kav, Birgit Strodel. J Chem Inf Model 2020
Suman Samantray, Feng Yin, Batuhan Kav, Birgit Strodel. J Chem Inf Model 2020
14
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
5
Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.
Phuong H Nguyen, Ayyalusamy Ramamoorthy, Bikash R Sahoo, Jie Zheng, Peter Faller, John E Straub, Laura Dominguez, Joan-Emma Shea, Nikolay V Dokholyan, Alfonso De Simone,[...]. Chem Rev 2021
Phuong H Nguyen, Ayyalusamy Ramamoorthy, Bikash R Sahoo, Jie Zheng, Peter Faller, John E Straub, Laura Dominguez, Joan-Emma Shea, Nikolay V Dokholyan, Alfonso De Simone,[...]. Chem Rev 2021
5
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
5
Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks.
Jack Hanson, Kuldip Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou. Bioinformatics 2019
Jack Hanson, Kuldip Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou. Bioinformatics 2019
5
4
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
4
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R Shirts, Jeremy C Smith, Peter M Kasson, David van der Spoel,[...]. Bioinformatics 2013
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R Shirts, Jeremy C Smith, Peter M Kasson, David van der Spoel,[...]. Bioinformatics 2013
4
Comparative Protein Structure Modeling Using MODELLER.
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
4
Using circular dichroism spectra to estimate protein secondary structure.
Norma J Greenfield. Nat Protoc 2006
Norma J Greenfield. Nat Protoc 2006
4
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
4
Protein secondary structure prediction based on position-specific scoring matrices.
D T Jones. J Mol Biol 1999
D T Jones. J Mol Biol 1999
4
The PSIPRED Protein Analysis Workbench: 20 years on.
Daniel W A Buchan, David T Jones. Nucleic Acids Res 2019
Daniel W A Buchan, David T Jones. Nucleic Acids Res 2019
4
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.
Matthias Heinig, Dmitrij Frishman. Nucleic Acids Res 2004
Matthias Heinig, Dmitrij Frishman. Nucleic Acids Res 2004
4
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
4
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
4
Scoring function for automated assessment of protein structure template quality.
Yang Zhang, Jeffrey Skolnick. Proteins 2004
Yang Zhang, Jeffrey Skolnick. Proteins 2004
4
HH-suite3 for fast remote homology detection and deep protein annotation.
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J Haunsberger, Johannes Söding. BMC Bioinformatics 2019
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J Haunsberger, Johannes Söding. BMC Bioinformatics 2019
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.